- a4Base::nlcvTTData to Demonstrate nlcv and Co Functions
- ABSSeq::simuN5Simulated study with random outliers
- acde::phytophthoraGene Expression Data for Tomato Plants Inoculated with _Phytophthora infestans_
- ACE::copyNumbersSegmentedSegmented data of two tumor samples
- aCGH::colorectalColorectal array CGH dataset
- aCGH::ex.acgh.hmmClass aCGH
- ACME::example.agffAn example ACME data structure of class ACMESet
- ADaCGH2::inputExA fictitious aCGH data set
- ADaCGH2::inputEx-spA fictitious aCGH data set
- ADAM::ExpressionAedesAedes aegypti RNA-seq data expression
- ADAM::KeggPathwaysAedesRelation between Aedes aegypti genes and KEGG pathways as ADAM input
- ADAMgui::DiffAedesAedes aegypti RNA-seq differential expression data example
- ADAMgui::GeneFunctionAedesRelation between Aedes aegypti genes and KEGG pathways
- ADAMgui::ResultAnalysisAedesResult from an example of ADAM Aedes aegypti analysis
- ADImpute::demo_dataSmall dataset for example purposes
- ADImpute::demo_netSmall regulatory network for example purposes
- ADImpute::demo_sceSmall dataset for example purposes
- ADImpute::network.coefficientsTranscriptome wide gene regulatory network
- ADImpute::transcript_lengthTable for transcript length calculations
- adSplit::golubKEGGSplitsExamplar splitSet
- AffiXcan::exprMatrixExpression data of two genes for 229 individuals
- AffiXcan::regionAssocAssociations between regulatory regions and expressed genes
- AffiXcan::trainingCovariatesCovariates of the population structure for 229 individuals
- affy::SpikeInSpikeIn Experiment Data: ProbeSet Example
- affy::cdfenv.exampleExample cdfenv
- affy::mapCdfNameClean Affymetrix's CDF name
- affycomp::dilution.phenodataPhenotypic Information for Dilution Study
- affycomp::hgu133a.spikein.phenodataphenotypic information for HGU133A spike in study
- affycomp::hgu133a.spikein.xhybCross hybridizers
- affycomp::mas5.assessmentExample of the result of assessments
- affycomp::spikein.phenodataphenotypic information for spike in study
- AGDEX::agdex.resSaved result returned by agdex()
- AGDEX::gset.dataa sample gene-set data
- AGDEX::human.dataSample ExpressionSet object of human data
- AGDEX::map.dataProbe-set Mapping Data
- AGDEX::mouse.dataMouse Data
- aggregateBioVar::small_airwaySmall Airway 'SingleCellExperiment' object
- AgiMicroRna::dd.microdata example (uRNAList)
- AgiMicroRna::ddPROCProcessed miRNA data (uRNAList)
- AgiMicroRna::targets.microExample of target file
- AIMS::AIMSmodelThe AIMS model
- AIMS::mcgillExampleSample of a breast cancer gene expression dataset generated at McGill University
- ALDEx2::selexSelection-based differential sequence variant abundance dataset
- ALDEx2::synth2Synthetic asymmetric dataset
- AllelicImbalance::ASEsetASEset objects
- AllelicImbalance::ASEset.simASEset.sim object
- AllelicImbalance::GRvariantsGRvariants object
- AllelicImbalance::genomatrixgenomatrix object
- AllelicImbalance::readsreads object
- AlpsNMR::HMDB_bloodThe Human Metabolome DataBase multiplet table: blood metabolites normally found in NMR-based metabolomics
- AlpsNMR::HMDB_cellThe Human Metabolome DataBase multiplet table: cell metabolites normally found in NMR-based metabolomics
- AlpsNMR::HMDB_urineThe Human Metabolome DataBase multiplet table: urine metabolites normally found in NMR-based metabolomics
- AlpsNMR::Parameters_bloodto rDolphin
- AlpsNMR::Parameters_cellParameters for cell samples profiling
- AlpsNMR::Parameters_urineParameters for urine samples profiling
- AlpsNMR::ROI_bloodROIs for blood (plasma/serum) samples
- AlpsNMR::ROI_cellROIs for cell samples
- AlpsNMR::ROI_urineROIs for urine samples
- AlpsNMR::hmdbThe Human Metabolome DataBase multiplet table
- altcdfenvs::cdfenvExCdfEnvAffy
- AMARETTO::BatchDataBatchData
- AMARETTO::Driver_GenesDriver_Genes
- AMARETTO::MsigdbMappingMsigdbMapping
- AMARETTO::ProcessedDataLIHCProcessedDataLIHC
- Anaquin::RnaQuinGeneMixtureRnaQuin mixture (gene level)
- Anaquin::RnaQuinIsoformMixtureRnaQuin mixture (isoform level)
- Anaquin::UserGuideData_5.4.5.1Section 5.4.5.1 Assembly Dataset
- Anaquin::UserGuideData_5.4.6.3Gene expression (RnaQuin)
- Anaquin::UserGuideData_5.6.3Differential expression (RnaQuin)
- ANCOMBC::QMPQuantitative Microbiome Project data
- annaffy::aafExprSample ExpressionSet used for demonstration purposes
- annotate::hgByChromsA dataset to show the human genome base pair locations per chromosome.
- annotate::hgCLengthsA dataset which contains the lengths (in base pairs) of the human chromosomes.
- annotate::hgu95AProbLocschromLocation instance hgu95AProbLocs, an example of a chromLocation object
- annotate::hgu95AchrolocAnnotation data for the Affymetrix HGU95A GeneChip
- annotate::hgu95AchromAnnotation data for the Affymetrix HGU95A GeneChip
- annotate::hgu95AllAnnotation data for the Affymetrix HGU95A GeneChip
- annotate::hgu95AsymAnnotation data for the Affymetrix HGU95A GeneChip
- annotationTools::annot_HGU133Aannot\_HGU133A
- annotationTools::orthoortho
- annotationTools::table_humantable\_human
- annotationTools::table_mousetable\_mouse
- annotatr::annotationsexample_annotations data
- anota::anotaDataPSample data set for anota
- anota::anotaDataTSample data set for anota
- anota::anotaPhenoVecSample data set for anota
- anota2seq::anota2seq_data_PSample data set for anota2seq
- anota2seq::anota2seq_data_TSample data set for anota2seq
- anota2seq::anota2seq_pheno_vecSample data set for anota2seq
- AnVILBilling::demo_reca demonstration avReckoning object
- apComplex::HMSPCIHigh-Throughput Mass Spectromic Protein Complex Identification (HMS-PCI) Data from Ho, et al. (2002)
- apComplex::HMSPCIgraphHigh-Throughput Mass Spectromic Protein Complex Identification (HMS-PCI) Data from Ho, et al. (2002)
- apComplex::KroganHigh-Definition Macromolecular Composition of Yeast RNA-Processing Complexes (2004)
- apComplex::MBMEcHMSPCIHMSPCI data complex estimates
- apComplex::MBMEcKroganKrogan data complex estimates
- apComplex::MBMEcTAPTAP data complex estimates
- apComplex::SBMHcHMSPCIHMSPCI data complex estimates
- apComplex::SBMHcTAPTAP data complex estimates
- apComplex::TAPTandem Affinity Purification (TAP) Data from Gavin et al. (2002)
- apComplex::TAPgraphTandem Affinity Purification (TAP) Data from Gavin et al. (2002)
- apComplex::UnRBBcHMSPCIHMSPCI data complex estimates
- apComplex::UnRBBcTAPTAP data complex estimates
- apComplex::apEXExample data set for apComplex package
- apComplex::apEXGExample data set for apComplex package
- apComplex::gavin06FilteredEstimatesAP-MS data complex estimates
- apComplex::gavinBP2006Tandem Affinity Purification (TAP) Data from Gavin et al. (2006)
- apComplex::krogan06FilteredEstimatesAP-MS data complex estimates
- apComplex::kroganBPMat2006Tandem Affinity Purification (TAP) Data from Krogan et al. (2006)
- apComplex::yNameTAPTAP data complex estimates using standard gene names
- apComplex::yTAPyTAP Complexes published Gavin, et al. (2002).
- arrayMvout::afxsubDEGMultivariate outlier detection based on PCA of QA statistics
- arrayMvout::fig3mapMultivariate outlier detection based on PCA of QA statistics
- arrayMvout::ilmQAMultivariate outlier detection based on PCA of QA statistics
- arrayMvout::itnQAMultivariate outlier detection based on PCA of QA statistics
- arrayMvout::maqcQAMultivariate outlier detection based on PCA of QA statistics
- arrayMvout::s12cDEGMultivariate outlier detection based on PCA of QA statistics
- arrayMvout::spikQAMultivariate outlier detection based on PCA of QA statistics
- arrayQuality::HsReferenceDBReference slides for Mouse oligos hybridizations
- arrayQuality::MmDEGenesKnown DE genes for Mouse quality hybridizations.
- arrayQuality::MmReferenceDBReference slides for Mouse oligos hybridizations
- ARRmNormalization::ProbesTypeProbe Design information for the 450k methylation assay
- artMS::artms_configartMS configuration template
- artMS::artms_data_corum_mito_databaseCORUM Protein Complexes database use for complex enrichment analysis
- artMS::artms_data_pathogen_LPNLPN PATHOGEN: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) UNIPROT IDS
- artMS::artms_data_pathogen_TBTB PATHOGEN: Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) UNIPROTS IDS
- artMS::artms_data_ph_configartMS configuration for the available PH dataset
- artMS::artms_data_ph_contrastContrast example for the PH dataset
- artMS::artms_data_ph_evidenceEvidence file example
- artMS::artms_data_ph_keysKeys File Example
- artMS::artms_data_ph_msstats_modelqcMSstats modelQC example
- artMS::artms_data_ph_msstats_resultsMSstats results example
- artMS::artms_data_randomDFRandom data set
- ASAFE::adm_ancestries_testAncestries of 250 admixed individuals at 6 SNPs
- ASAFE::adm_genotypes_testGenotypes of 250 admixed individuals at 6 markers
- ASGSCA::B0Matrix indicating connections between the latent variables for QCAHS data.
- ASGSCA::GenPhenDataset to test GSCAestim and GSCA functions.
- ASGSCA::QCAHSDataset used in the vignette.
- ASGSCA::ResQCAHSA list containing the results obtained for the QCAHS dataset.
- ASGSCA::W0Matrix indicating connections between the observed variables and the latent variables for QCAHS data.
- ASICS::pure_libraryPure spectra library
- ASSET::N00Data for the h.traits example
- ASSET::N10Data for the h.traits example
- ASSET::N11Data for the h.traits example
- ASSET::NeffData for the fast_asset example
- ASSET::SEData for the fast_asset example
- ASSET::SNPData for the fast_asset example
- ASSET::betahatData for the fast_asset example
- ASSET::dataData for the h.traits example
- ASSET::dataData for the h.traits example
- ASSET::ldscintmatData for the fast_asset example
- ASSET::traitsData for the fast_asset example
- ASSIGN::excludegenesExclude Gene List
- ASSIGN::geneList1Pathway signature gene sets
- ASSIGN::gfrn_geneListPathway Signature Gene Lists
- ASSIGN::testData1Gene expression profiling from cancer patients (test dataset)
- ASSIGN::trainingData1Gene expression profiling from cell line perturbation experiments (training dataset)
- ASURAT::human_COMSig_egA list of small Cell Ontology and MSigDB databases for human.
- ASURAT::human_GO_egA list of small Gene Ontology database for human.
- ASURAT::human_KEGG_egA list of small KEGG database for human.
- ASURAT::pbmc_egA SingleCellExperiment object made from a gene expression table.
- ASURAT::pbmcs_egA list of SingleCellExperiment objects made from sign-sample matrices.
- ATACCoGAPS::exampleMotifListExample list of motifs for examples
- ATACCoGAPS::schepCellTypesCell types corresponding to subsetSchepData
- ATACCoGAPS::schepCogapsResultCogapsResult from the subsetSchepData object
- ATACCoGAPS::schepGrangesGRanges corresponding to subsetSchepData
- ATACCoGAPS::schepPeaksPeaks corresponding to subsetSchepData
- ATACCoGAPS::subsetSchepDataSmall subset of the scATAC-seq data from Schep et al, 2017, Nature Methods paper.
- ATACCoGAPS::tfDataList of human TFs and motifs from cisBP database
- atSNP::encode_motifA motif library containing 2065 motifs downloaded from http://compbio.mit.edu/encode-motifs/motifs.txt.
- atSNP::encode_motifinfoThe information for the motif library downloaded from http://compbio.mit.edu/encode-motifs/motifs.txt.
- atSNP::jaspar_motifA motif library containing 593 motifs downloaded from http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant/pfm_all .txt.
- atSNP::jaspar_motifinfoThe information for the motif library downloaded from http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant/pfm_all .txt.
- atSNP::motif_libraryA sample motif library.
- atSNP::motif_matchComposit logo plotting input containing motif scores, the matching subsequences and the augmented matching subsequences on SNP and reference allele
- atSNP::motif_scoresScores for the sample snp data computed based on the motif data.
- atSNP::priorDefault stationary distribution for nucleotide sequences in the reference genome.
- atSNP::snpInfoA data set for SNP information.
- atSNP::snp_tblA data frame for SNP information.
- atSNP::transitionDefault transition probability matrix for nucleotide sequences in the reference genome.
- attract::exprs.datGene Expression Matrix of Published Data
- attract::loring.esetAn ExpressionSet Object containing published data from M?ller et al.
- attract::samp.infosamp.info Contains the Sample Information for the Mueller data set.
- attract::subset.loring.esetAn ExpressionSet Object containing published data from M?ller et al.
- AWFisher::data_mouseMetabolismMouse metabolism microarray data
- BaalChIP::BaalObjectBaalObject example dataset
- BaalChIP::ENCODEexampleENCODEexample example dataset
- BaalChIP::FAIREexampleFAIREexample example dataset
- BaalChIP::UniqueMappability50bp_hg19Genomic regions of unique mappability
- BaalChIP::blacklist_hg19Blacklisted genomic regions
- BaalChIP::pickrell2011cov1_hg19Genomic regions of collapsed repeats
- BAGS::AnnotationMFGOList containing a collection of gene symbols with their associated GO term for the Molecular function ontology
- ballgown::bgToy ballgown object
- BANDITS::gene_tr_idGene-transcript matching
- BANDITS::input_dataA 'BANDITS_data' object, generated with 'create_data'
- BANDITS::precisionEstimates for the log-precision parameter, generated with 'prior_precision'
- BANDITS::resultsResults of the DTU test, generated with 'test_DTU'
- Banksy::hippocampusMouse Hippocampus VeraFISH data
- Banksy::ringsAn unrealistic simulation of spatially-resolved omics data.
- banocc::compositions_hard_nullSimulated compositional data with no feature correlations
- banocc::compositions_neg_spikeSimulated compositional data with a negative count correlation
- banocc::compositions_nullSimulated compositional data with no feature correlations
- banocc::compositions_pos_spikeSimulated compositional data with a positive count correlation
- banocc::counts_hard_nullSimulated count data with no feature correlations
- banocc::counts_neg_spikeSimulated count data with one negative feature correlation
- banocc::counts_nullSimulated count data with no feature correlations
- banocc::counts_pos_spikeSimulated count data with one positive feature correlation
- barcodetrackR::wu_subsetSmall subset of Wu barcoding dataset
- BaseSpaceR::aAuthSample 'AppAuth' instance with 'browse global' scope
- Basic4Cseq::liverDataExample 4C-seq data set of fetal liver data
- Basic4Cseq::liverDataRawExample 4C-seq data set of fetal liver data
- BASiCS::ChainRNAExtract from the chain obtained for the Grun et al (2014) data: pool-and-split samples
- BASiCS::ChainRNARegExtract from the chain obtained for the Grun et al (2014) data: pool-and-split samples (regression model)
- BASiCS::ChainSCExtract from the chain obtained for the Grun et al (2014) data: single-cell samples
- BASiCS::ChainSCRegExtract from the chain obtained for the Grun et al (2014) data: single-cell samples (regression model)
- BatchQC::batch_indicatorBatch and Condition indicator for signature data
- BatchQC::protein_dataProtein data with 39 protein expression levels
- BatchQC::protein_sample_infoBatch and Condition indicator for protein expression data
- BatchQC::signature_dataSignature data with 1600 gene expression levels
- BayesKnockdown::lincs.kdLINCS L1000 Knockdown Example Dataset
- bayNorm::EXAMPLE_DATA_listA subset of Grun et al (2014) data: 2i samples
- baySeq::CDPost'countData' object derived from data file 'simData' with estimated likelihoods of differential expression.
- baySeq::CDPriors'countData' object derived from data file 'simData' with estimated priors.
- baySeq::mobAnnotationAnnotation data for a set of small RNA loci derived from sequencing of grafts of Arabidopsis thaliana intended for differential expression analyses.
- baySeq::mobDataData from a set of small RNA sequencing experiments carried out on grafts of Arabidopsis thaliana intended for differential expression analyses.
- baySeq::pairDataSimulated data for testing the baySeq package methods for paired data
- baySeq::simDataSimulated data for testing the baySeq package methods
- baySeq::zimDataSimulated data for testing the baySeq package methods
- BCRANK::BCRANKoutBCRANK results for USF1 ChIP-chip data
- beadarray::metaTemplateGEO required fields
- beadarray::platformSigsAnnotation definitions
- BEARscc::BEAR_analyzed.sceBEARscc downstream example objects.
- BEARscc::BEAR_examples.sceExample data for BEARscc.
- BEARscc::BEARscc_clusts.dfBEARscc downstream example objects.
- BEARscc::ERCC.counts.dfExample data for BEARscc.
- BEARscc::ERCC.meta.dfExample data for BEARscc.
- BEARscc::clusters.dfBEARscc downstream example objects.
- BEARscc::data.counts.dfExample data for BEARscc.
- BEARscc::noise_consensusBEARscc downstream example objects.
- BEARscc::reclusterBEARscc downstream example objects.
- BEAT::positionsSample dataset of CpG positions for a single cell BS-seq sample
- BEAT::positions.referenceSample dataset of CpG positions for a reference BS-Seq sample
- BEclear::ex.corrected.dataExample matrix of corrected data for the BEclear-package
- BEclear::ex.dataExample data set for the BEclear-package
- BEclear::ex.samplesExample data set for the BEclear-package
- benchdamic::microbial_metabolism(Data) Microbial metabolism
- benchdamic::ps_plaque_16S(Data) 60 Gingival Plaque samples of 16S rRNA (HMP 2012)
- benchdamic::ps_stool_16S(Data) 33 Stool samples of 16S rRNA (HMP 2012)
- betaHMM::annotation_dataMethylationEPIC manifest data.
- betaHMM::pca_methylation_dataSimulated DNA methylation data
- betaHMM::sample_annotation_fileMethylationEPIC manifest data.
- betaHMM::sample_methylation_fileSimulated DNA methylation data
- BG2::SNPsA. Thaliana Genotype matrix
- BG2::Y_binaryA. Thaliana Simulated Phenotype matrix
- BG2::Y_poissonA. Thaliana Simulated Phenotype matrix
- BG2::kinshipA. Thaliana Kinship matrix
- BgeeDB::geneListExample of gene list object used to run a topAnat enrichment test, created on June 2018. The format of the gene list is the same as the gene list required to build a 'topGOdata' object in the 'topGO' package: a vector with background genes as names, and 0 or 1 values depending if a gene is in the foreground or not. In this example the foreground genes are zebrafish genes with an annotated phenotype related to "pectoral fin", and the background is composed of all zebrafish Ensembl genes with an annotated phenotype from ZFIN. The gene list was built using the biomaRt package, and the code used can be found in the vignette of the package.
- BicARE::sample.bicDataExample data set for BicARE
- BicARE::sample.biclusteringExample biclustering object
- BiGGR::E.coli_iAF1260Ecoli dataset with ORFs and thermodynamic information
- BiGGR::E.coli_iJR904Ecoli genome-scale model
- BiGGR::E.coli_textbookEcoli dataset from the BiGG database
- BiGGR::GlycolysisMetabolic reconstruction of Glycolysis pathway
- BiGGR::H.pylori_ilT341H.pylori in silico genome-scale characterization of single and double deletion mutants
- BiGGR::H.sapiens_Recon_1Reconstruction of human metabolism from the BiGG database
- BiGGR::M.barkeri_iAF692Metabolic reconstruction of M.barkeri from the BiGG database
- BiGGR::M.tuberculosis_iNJ661Metabolic reconstruction of M.tuberculosis from the BiGG database
- BiGGR::P.putida_iJN746Metabolic reconstruction of P.putida from the BiGG database
- BiGGR::Recon2Human metabolic reconstruction Recon2
- BiGGR::S.aureus_iSB619Metabolic reconstruction of S.aureus from the BiGG database
- BiGGR::S.cerevisiae_iND750Metabolic reconstruction of S.cerevisiae from the BiGG database
- BiGGR::lying.tunell.dataDataset of in vivo cerebral metabolite uptake and release rates in healthy humans (old subjects)
- bigmelon::cantaloupeSmall MethyLumi 450k data sets for testing
- bigmelon::honeydewSmall MethyLumi 450k data sets for testing
- bioassayR::samplebioassaySample activity data for use with bioassayR
- Biobase::SWClass to Contain High-Throughput Assays and Experimental Metadata
- Biobase::aaMapDataset: Names and Characteristics of Amino Acids
- Biobase::geneCovSample expression matrix and phenotype data.frames.
- Biobase::geneCovariateSample expression matrix and phenotype data.frames.
- Biobase::geneDataSample expression matrix and phenotype data.frames.
- Biobase::reporterExample data.frame representing reporter information
- Biobase::sample.ExpressionSetDataset of class 'ExpressionSet'
- Biobase::sample.MultiSetData set of class 'MultiSet'
- Biobase::seDSample expression matrix and phenotype data.frames.
- biobroom::hammerExpressionSet results from Hammer et al 2010
- bioCancer::epiGenomicsDefault dataset of bioCancer
- bioCancer::user_CNAExample of Copy Number Alteration (CNA) dataset
- bioCancer::user_MetHM27Example of Methylation HM27 dataset
- bioCancer::user_MetHM450Example of Methylation HM450 dataset
- bioCancer::user_MutExample of Mutation dataset
- bioCancer::user_mRNAExample of mRNA expression dataset
- BioCartaImage::BC2ENTREZPre-computed data objects
- BioCartaImage::BIOCARTA_PATHWAYSPre-computed data objects
- BioCartaImage::PATHWAY2BCPre-computed data objects
- BioCartaImage::PATHWAY2ENTREZPre-computed data objects
- BioCartaImage::PATHWAY2MSIGDBPre-computed data objects
- BiocFHIR::allincollection of synthea FHIR documents ingested
- BiocHail::kg_3202data.frame with metadata about 3202 samples genotyped against T2T reference
- BiocHail::pcs_191kHWE-normalized PCA scores for 3202 thousand-genomes samples genotyped with the telomere-to-telomere reference
- BiocHail::pcs_38kHWE-normalized PCA scores for 3202 thousand-genomes samples genotyped with the telomere-to-telomere reference
- biocViews::biocViewsVocabBioconductor Task Views Vocabulary Data
- biomvRCNS::coriellArray CGH data set of Coriell cell lines
- biomvRCNS::encodeTP53mapped RNA-seq data from ENCODE
- biomvRCNS::variosmDifferential methylation data from sequencing
- BioNAR::diseasomeBarabasi's Diseasome Network
- BioNERO::filt.seFiltered maize gene expression data from Shin et al., 2021.
- BioNERO::og.zma.osaOrthogroups between maize and rice
- BioNERO::osa.seRice gene expression data from Shin et al., 2021.
- BioNERO::zma.interproMaize Interpro annotation
- BioNERO::zma.seMaize gene expression data from Shin et al., 2021.
- BioNERO::zma.tfsMaize transcription factors
- BioNet::pvaluesExampleExample p-values for aggregation statistics
- biosigner::diaplasmaAnalysis of plasma from diabetic patients by LC-HRMS
- Biostrings::HNF4alphaKnown HNF4alpha binding sequences
- Biostrings::yeastSEQCHR1An annotation data file for CHR1 in the yeastSEQ package
- BioTIP::GSE6136_cliGSE6136 cli dataset
- BioTIP::GSE6136_matrixGSE6136 matrix dataset
- BioTIP::ILEFChromosome ranges of chr21 dataset
- BioTIP::codcod dataset
- BioTIP::gencodeA chr21 data from GENCODE GRCh37
- BioTIP::intronCoding transcriptome in chr21 dataset
- BioTIP::membersL
- BioTIP::subcounts
- biovizBase::crc.grCRC
- biovizBase::crc1.GeRLcrc1.GeRL
- biovizBase::darned_hg19_subset500Subset of RNA editing sites in hg19...
- biovizBase::genesymbolGene symbols with position...
- biovizBase::hg19IdeogramHg19 ideogram without cytoband information...
- biovizBase::hg19IdeogramCytoHg19 ideogram with cytoband information...
- biovizBase::hg19subCRC
- biovizBase::ideoideogram without cytoband information
- biovizBase::ideoCytoideogram with cytoband information
- biovizBase::mut.grCRC
- BiRewire::BRCA_binary_matrixTCGA Brest Cancer data
- BiRewire::test_dsgTool example of dsg
- biscuiteer::ENSR_subset.hg19ENSR_subset data from hg19 genome
- biscuiteer::ENSR_subset.hg38ENSR_subset data from hg38 genome
- biscuiteer::GRCh37.chromArmGRCh37.chromArm
- biscuiteer::GRCh38.chromArmGRCh38.chromArm
- biscuiteer::H9state23unmeth.hg19H9state23unmeth.hg19
- biscuiteer::H9state23unmeth.hg38H9state23unmeth.hg38
- biscuiteer::HMM_CpG_islands.hg19HMM_CpG_islands.hg19
- biscuiteer::HMM_CpG_islands.hg38HMM_CpG_islands.hg38
- biscuiteer::clocksclocks
- biscuiteer::hg19.chromArmhg19.chromArm
- biscuiteer::hg38.chromArmhg38.chromArm
- biscuiteer::seqinfo.hg19seqinfo.hg19
- biscuiteer::seqinfo.hg38seqinfo.hg38
- biscuiteer::seqinfo.mm10seqinfo.mm10
- BiSeq::DMRsThe output of 'findDMRs'
- BiSeq::betaResultsThe output of 'betaRegression'
- BiSeq::betaResultsNullThe output of 'betaRegression' for resampled data
- BiSeq::predictedMethThe output of 'predictMeth'
- BiSeq::promotersA 'GRanges' of promoters of the human genome
- BiSeq::rrbsRRBS data of APL patient samples and controls.
- BiSeq::varioOutput of 'makeVariogram'
- blacksheepr::sample_annotationdatasample_annotationdata
- blacksheepr::sample_phosphodatasample_phosphodata
- blacksheepr::sample_rnadatasample_rnadata
- BLMA::data_GSE17054Gene expression dataset GSE17054 from Majeti et al.
- BLMA::data_GSE33223Gene expression dataset GSE33223 from Bacher et al.
- BLMA::data_GSE42140The gene expression dataset GSE42140 obtained from Gene Expression Omnibus
- BLMA::data_GSE57194Gene expression dataset GSE57194 from Abdul-Nabi et al.
- BLMA::group_GSE17054Gene expression dataset GSE17054 from Majeti et al.
- BLMA::group_GSE33223Gene expression dataset GSE33223 from Bacher et al.
- BLMA::group_GSE42140The gene expression dataset GSE42140 obtained from Gene Expression Omnibus
- BLMA::group_GSE57194Gene expression dataset GSE57194 from Abdul-Nabi et al.
- bnbc::cgExSample chr22 Data
- bnem::bcrB-Cell receptor signalling perturbations
- BOBaFIT::TCGA_BRCA_CN_segmentsSegments of 100 Breast Cancer samples, downloaded from TCGA-BRCA.
- BPRMeth::bernoulli_dataSynthetic Bernoulli data
- BPRMeth::beta_dataSynthetic Beta data
- BPRMeth::binomial_dataSynthetic Binomial data
- BPRMeth::encode_exprProcessed ENCODE expression data
- BPRMeth::encode_metProcessed ENCODE methylation data
- BPRMeth::gaussian_dataSynthetic Gaussian data
- BPRMeth::gex_dataSynthetic expression data
- BPRMeth::meth_dataSynthetic bulk methylation data
- brendaDb::acronymsInformation fields and their corresponding acronyms.
- BRGenomics::PROseqPRO-seq data from Drosophila S2 cells
- BRGenomics::PROseq_pairedPRO-seq data from Drosophila S2 cells
- BRGenomics::txs_dm6_chr4Ensembl transcripts for Drosophila melanogaster, dm6, chromosome 4.
- bsseq::BS.chr22Whole-genome bisulfite sequencing for chromosome 22 from Lister et al.
- BubbleTree::all.somatic.lstall.somatic.lst
- BubbleTree::allCNV.lstallCNV.lst
- BubbleTree::allCall.lstallCall.lst
- BubbleTree::allHetero.lstallHetero.lst
- BubbleTree::allRBD.lstallRBD.lst
- BubbleTree::cancer.genes.minus2cancer.genes.minus2.rda
- BubbleTree::centromere.datcentromere.dat
- BubbleTree::cnv.grcnv.gr
- BubbleTree::cyto.grcyto.gr
- BubbleTree::gene.uni.clean.grgene.uni.clean.gr
- BubbleTree::hg19.seqinfohg19.seqinfo.Rd
- BubbleTree::snp.grsnp.gr
- BubbleTree::vol.genesvol.genes
- BUMHMM::covFileExample coverage data set.
- BUMHMM::docFileExample drop-off count data set.
- BUMHMM::dorFileExample drop-off rate data set.
- BUMHMM::seExample RNA structure probing data set.
- BUMHMM::seqExample genomic sequence string.
- bumphunter::TTExample data
- BUS::copasicopasi data
- BUS::tumors.mRNAGene expression data from Human brain tumors
- BUS::tumors.miRNAmiRNA data from Human brain tumors
- BUScorrect::BUSexample_dataA simulated data set
- BUSpaRse::cellranger_biotypesCell Ranger gene biotypes
- BUSpaRse::ensembl_gene_biotypesGene biotypes from Ensembl
- BUSpaRse::ensembl_gff_mcolsThese are the column names of the 'mcols' when the Ensembl GTF file is read into R as a 'GRanges', including 'gene_id', 'transcript_id', 'biotype', 'description', and so on, and the mandatory tags like 'ID', 'Name', and 'Parent'.
- BUSpaRse::ensembl_gtf_mcolsTags in the attributes field of Ensembl GTF files
- BUSpaRse::ensembl_tx_biotypesTranscript biotypes from Ensembl
- BUSpaRse::refseq_gff_mcolsTags in the attributes field of RefSeq GFF files
- BUSseq::BUSseqfits_exampleAn external example of the output of the 'BUSseq_MCMC'
- CaDrA::BRCA_GISTIC_MUT_SIGGenomic Data from TCGA BRCA MUT + GISTIC
- CaDrA::CCLE_MUT_SCNAGenomic Data from CCLE MUT + SCNA
- CaDrA::CTNBB1_reporterTranscriptional Activity of Beta-Catenin in Cancers
- CaDrA::TAZYAP_BRCA_ACTIVITYYAP/TAZ Activity in TCGA BRCA dataset
- CaDrA::perm_resPre-computed permutation results for simulated data ('sim_FS')
- CaDrA::sim_FSSimulated Genomic Data
- CaDrA::sim_ScoresSimulated Input Scores
- CaDrA::topn_listTop-N Results for Simulated Data ('sim_FS')
- CAEN::realDataA real dataset of gene expression RNA-seq.
- CAFE::CAFE_dataCAFE data set
- CAGEfightR::exampleBidirectionalExample CAGE Data
- CAGEfightR::exampleCTSSsExample CAGE Data
- CAGEfightR::exampleDesignExample CAGE Data
- CAGEfightR::exampleGenesExample CAGE Data
- CAGEfightR::exampleUnidirectionalExample CAGE Data
- cageminer::chr_lengthPepper chromosome lengths
- cageminer::gcnSimulation of the output list from BioNERO::exp2gcn() with pepper data
- cageminer::gene_rangesGenomic coordinates of pepper genes
- cageminer::guidesGuide genes associated with defense and resistance to oomycetes
- cageminer::hubsExample hub genes for the network stored in the gcn object
- cageminer::mine2Example output from mine_step2()
- cageminer::mined_candidatesExample output from mined_candidates()
- cageminer::pepper_seGene expression data from Kim et al., 2018.
- cageminer::snp_posCapsicum annuum SNPs associated with resistance to Phytophthora root rot.
- cageminer::tfsPepper transcription factors
- CAGEr::FANTOM5humanSamplesFANTOM5 human samples
- CAGEr::FANTOM5mouseSamplesFANTOM5 mouse samples
- CAGEr::exampleCAGEexpExample CAGEexp object.
- CAGEr::exampleZv9_annotExample zebrafish annotation data
- calm::psoPsoriasis RNA-seq dataset
- CAMERA::mm14Extract of marker mixture 14 LC/MS data
- cancerclass::GOLUBGOLUB DATA
- cancerclass::GOLUB1GOLUB DATA
- cardelino::A_cloneA matrix of read numbers of alternative alleles for clone ID
- cardelino::A_germlineA matrix of read numbers of alternative alleles
- cardelino::Config_allA list of tree configuration
- cardelino::D_cloneA matrix of sequencing depths for clone ID
- cardelino::D_germlineA matrix of sequencing depths
- cardelino::D_inputA matrix of sequencing depths
- cardelino::treeA tree object
- cardelino::tree_3cloneA tree object
- cardelino::tree_4cloneA tree object
- cardelino::tree_5cloneA tree object
- casper::K562.r1l1Toy RNA-seq data from RGASP project.
- casper::distrsGSE37704Estimated read start and insert size distributions from MiSeq data in GEO dataset GSE37704.
- casper::hg19DBSubset of human genome (UCSC hg19 version)
- CATALYST::PBMC_fsExample data sets
- CATALYST::PBMC_mdExample data sets
- CATALYST::PBMC_panelExample data sets
- CATALYST::isotope_listExample data sets
- CATALYST::merging_tableExample data sets
- CATALYST::mp_cellsExample data sets
- CATALYST::raw_dataExample data sets
- CATALYST::sample_ffExample data sets
- CATALYST::sample_keyExample data sets
- CATALYST::ss_expExample data sets
- categoryCompare::ccOptsTest data for 'categoryCompare'
- categoryCompare::ccResultsTest data for 'categoryCompare'
- categoryCompare::ccResultsBPHierTest data for 'categoryCompare'
- categoryCompare::enrichListsTest data for 'categoryCompare'
- categoryCompare::gUniverseTest data for 'categoryCompare'
- categoryCompare::geneListsTest data for 'categoryCompare'
- categoryCompare::gseaResTest data for 'categoryCompare'
- categoryCompare::table10Test data for 'categoryCompare'
- categoryCompare::table48Test data for 'categoryCompare'
- CBEA::hmp_gingivalGingival data set from the Human Microbiome Project
- CBNplot::exampleEaResExample enrichment analysis result
- CBNplot::exampleGeneExpExample gene expression data
- CCPlotR::toy_dataToy data for CCPlotR
- CCPlotR::toy_expToy expression data for CCPlotR
- CCPROMISE::exmplESetExample of Conceptual Expression Set
- CCPROMISE::exmplGeneSetExample of Conceptual Gene Annotation
- CCPROMISE::exmplMSetExample of Conceptual Methylation Set
- CCPROMISE::exmplPatExample of Conceptual Phenotype Pattern Definition Set
- CDI::one_batch_matrixSimulated count matrix from one batch
- CDI::one_batch_matrix_celltypeCell type labels of simulated count matrix from one batch
- CDI::one_batch_matrix_label_dfClustering labels for simulated one-batch single-cell count matrix
- CDI::two_batch_matrixSimulated count matrix from two batches
- CDI::two_batch_matrix_batchBatch labels of simulated count matrix from two batches
- CDI::two_batch_matrix_celltypeCell type labels of simulated count matrix from two batches
- CDI::two_batch_matrix_label_dfClustering labels for simulated two-batch single-cell count matrix
- celaref::de_table.demo_queryDemo query de table
- celaref::de_table.demo_refDemo ref de table
- celaref::demo_cell_info_tableDemo cell info table
- celaref::demo_counts_matrixDemo count matrix
- celaref::demo_gene_info_tableDemo gene info table
- celaref::demo_microarray_exprDemo microarray expression table
- celaref::demo_microarray_sample_sheetDemo microarray sample sheet table
- celaref::demo_query_seDemo query se (summarizedExperiment)
- celaref::demo_ref_seDemo reference se (summarizedExperiment)
- celda::celdaCGGridSearchResceldaCGGridSearchRes
- celda::celdaCGModceldaCGmod
- celda::celdaCGSimceldaCGSim
- celda::celdaCModceldaCMod
- celda::celdaCSimceldaCSim
- celda::celdaGModceldaGMod
- celda::celdaGSimceldaGSim
- celda::contaminationSimcontaminationSim
- celda::sampleCellssampleCells
- celda::sceCeldaCsceCeldaC
- celda::sceCeldaCGsceCeldaCG
- celda::sceCeldaCGGridSearchsceCeldaCGGridSearch
- celda::sceCeldaGsceCeldaG
- CellBarcode::bc_objA dummy BarcodeObj object
- CellBench::sample_sce_dataThis is data for testing functions in CellBench.
- CelliD::HallmarkHallmark Pathways from MSigDB
- CelliD::HgProteinCodingGenesHomo Sapiens Protein Coding Genes
- CelliD::MgProteinCodingGenesMus Musculus Protein Coding Genes
- CelliD::seuratPbmcSeurat object of 400 PBMC cells
- cellity::extra_human_genesAdditional human genes that are used in feature extraction
- cellity::extra_mouse_genesAdditional mouse genes that are used in feature extraction
- cellity::feature_infoInformation which genes and GO categories should be included as features. Also defines which features are cell-type independent (common features)
- cellity::mES1_featuresReal test dataset containing all and common features from the paper (mES1)
- cellity::mES1_labelsReal test dataset containing annotation of cells
- cellity::param_mES_allParameters used for SVM classification
- cellity::param_mES_commonParameters used for SVM classification
- cellity::sample_countsSample gene expression data containing 40 cells
- cellity::sample_statsSample read statistics data containing 40 cells
- cellity::training_mES_featuresOriginal training dataset containing all and common features from the paper (training mES)
- cellity::training_mES_labelsOriginal training dataset containing annotation of cells
- CellMapper::ExampleQueryGenesExample Gene Lists
- CellMapper::NegativeControlGenesExample Gene Lists
- CellMapper::PositiveControlGenesExample Gene Lists
- cellmigRation::ThreeConditionsIntermediates and Results from Cell Tracking Analyses
- cellmigRation::TrackCellsDatasetSample Stack of Fluorescent Cells
- cellmigRation::TrajectoryDatasetTrajectories of 350 cells
- cellmigRation::WSADatasetTrajectories of 147 cells
- cellmigRation::preProcCellMigTrajectories of 11 cells
- CellNOptR::CNOlistDREAMData used for the DREAM3 challenge
- CellNOptR::CNOlistToyToy data
- CellNOptR::CNOlistToy2Toy data with 2 time points
- CellNOptR::CNOlistToyMMBToy data
- CellNOptR::DreamModelModel used for the DREAM3 challenge
- CellNOptR::ToyModelToy model
- CellNOptR::ToyModel2Toy model
- CellNOptR::cnodataGet data from a CellNOpt data repository
- CellNOptR::pknmodelpknmodel
- CellTrails::exSCEExample single-cell expression data
- CEMiTool::cemCEMiTool Object
- CEMiTool::expr0Yellow Fever gene expression data from GEO study GSE13485
- CEMiTool::sample_annotYellow Fever Sample Annotation data
- Cepo::cellbenchcellbench
- Cepo::sce_pancreassce_pancreas
- ceRNAnetsim::TCGA_E9_A1N5_mirnanormalTCGA_E9_A1N5_mirnanormal
- ceRNAnetsim::TCGA_E9_A1N5_mirnatumorTCGA_E9_A1N5_mirnatumor
- ceRNAnetsim::TCGA_E9_A1N5_normalTCGA_E9_A1N5_normal
- ceRNAnetsim::TCGA_E9_A1N5_tumorTCGA_E9_A1N5_tumor
- ceRNAnetsim::huge_examplehuge example
- ceRNAnetsim::midsampmidsamp
- ceRNAnetsim::midsamp_new_countsmidsamp_new_counts
- ceRNAnetsim::minsampminsamp
- ceRNAnetsim::mirtarbasegenemirtarbasegene
- ceRNAnetsim::new_countsnew_counts
- CeTF::CeTFdemoCeTFdemo class object example
- CeTF::RIF_inputRegulatory Impact Factors (RIF) input
- CeTF::TFsTranscripition Factors data
- CeTF::enrichdemoEnrichment data
- CeTF::refGenesList of reference genes for 5 different organisms to perform enrichment
- CeTF::simCountsSimulated counts data
- CeTF::simNormSimulated normalized data
- cfTools::CancerDetector.markersCancer-specific marker parameter
- cfTools::CancerDetector.readsFragment-level methylation state for cancer detection
- cfTools::CpG_OB_demoMethylation information for CpG on the original bottom strand (OB)
- cfTools::CpG_OT_demoMethylation information for CpG on the original top strand (OT)
- cfTools::beta_matrixBeta value matrix
- cfTools::cfDeconvolve.markersTissue-specific marker parameter
- cfTools::cfDeconvolve.readsFragment-level methylation state for tissue deconvolution
- cfTools::cfsort_markerscfSort markers
- cfTools::cfsort_readsFragment-level methylation state for cfSort tissue deconvolution
- cfTools::demo.fragment_level.meth.bedFragment-level methylation information
- cfTools::demo.refo_frag.bedFragment-level information
- cfTools::demo.refo_meth.bedMethylation information on fragments
- cfTools::demo.sorted.bedPaired-end sequencing reads
- cfTools::marker_indexMarker name
- cfTools::markers.bedGenomic postions of markers
- cfTools::sample_typeSample type
- CGEN::LocusMapDataLocus map data
- CGEN::XdataSample covariate and outcome data
- CGEN::Xdata2Sample covariate and outcome data
- CGHbase::WiltingCervical cancer arrayCGH data
- CGHbase::WiltingCalledCervical cancer arrayCGH data called with CGHcall
- CGHbase::WiltingNormNormalized log2 ratios from cervical cancer arrayCGH data.
- CGHbase::WiltingRawRaw log2 ratios from cervical cancer arrayCGH data.
- CGHbase::WiltingRegionsRegions of cervical cancer arrayCGH data as defined by CGHregions
- CGHbase::WiltingSegSegmented log2 ratios from cervical cancer arrayCGH data.
- CGHcall::WiltingCervical cancer arrayCGH data
- cghMCR::segDataThe constructor for the cghMCR class
- CGHnormaliter::LeukemiaArray CGH experiment data on childhood acute lymphoblastic leukemia (ALL) in humans
- ChemmineR::apfpFrequent Atom Pairs
- ChemmineR::apsetAtom pairs stored in 'APset' object
- ChemmineR::atompropStandard atomic weights
- ChemmineR::pubchemFPencodingEnncoding of PubChem Fingerprints
- ChemmineR::sdfsampleSD file in 'SDFset' object
- ChemmineR::smisampleSMILES file in 'SMIset' object
- CHETAH::headneck_refA SingleCellExperiment with celltypes in the "celltypes" colData. A subset of the Head-Neck data from Puram et al. (2017) Cancer Cell.
- CHETAH::input_melA SingleCellExperiment on which CHEATHclassifier is run using the 'headneck_ref' It holds subset of the Melanoma data, from Tirosh et al. (2016), Science.
- Chicago::cdUnitTestChicagoData object for unit testing
- ChIPanalyser::AccessChIPanalyserData
- ChIPanalyser::chipChIPanalyserData
- ChIPanalyser::csChIPanalyserData
- ChIPanalyser::geneRefChIPanalyserData
- ChIPanalyser::topChIPanalyserData
- ChIPComp::seqDataA 'ChIPComp' object.
- ChIPexoQual::blacklists'list' of 'GRanges' objects with the blacklists generated by the ENCODE and modENCODE projects.
- ChIPexoQual::exoExample'ExoData' results for FoxA1 ChIP-exo experiment
- ChIPpeakAnno::ExonPlusUtr.human.GRCh37Gene model with exon, 5' UTR and 3' UTR information for human sapiens (GRCh37) obtained from biomaRt
- ChIPpeakAnno::HOT.spotsHigh Occupancy of Transcription Related Factors regions
- ChIPpeakAnno::Peaks.Ste12.Replicate1Ste12-binding sites from biological replicate 1 in yeast (see reference)
- ChIPpeakAnno::Peaks.Ste12.Replicate2Ste12-binding sites from biological replicate 2 in yeast (see reference)
- ChIPpeakAnno::Peaks.Ste12.Replicate3Ste12-binding sites from biological replicate 3 in yeast (see reference)
- ChIPpeakAnno::TSS.human.GRCh37TSS annotation for human sapiens (GRCh37) obtained from biomaRt
- ChIPpeakAnno::TSS.human.GRCh38TSS annotation for human sapiens (GRCh38) obtained from biomaRt
- ChIPpeakAnno::TSS.human.NCBI36TSS annotation for human sapiens (NCBI36) obtained from biomaRt
- ChIPpeakAnno::TSS.mouse.GRCm38TSS annotation data for Mus musculus (GRCm38.p1) obtained from biomaRt
- ChIPpeakAnno::TSS.mouse.NCBIM37TSS annotation data for mouse (NCBIM37) obtained from biomaRt
- ChIPpeakAnno::TSS.rat.RGSC3.4TSS annotation data for rat (RGSC3.4) obtained from biomaRt
- ChIPpeakAnno::TSS.rat.Rnor_5.0TSS annotation data for Rattus norvegicus (Rnor_5.0) obtained from biomaRt
- ChIPpeakAnno::TSS.zebrafish.Zv8TSS annotation data for zebrafish (Zv8) obtained from biomaRt
- ChIPpeakAnno::TSS.zebrafish.Zv9TSS annotation for Danio rerio (Zv9) obtained from biomaRt
- ChIPpeakAnno::annotatedPeakAnnotated Peaks
- ChIPpeakAnno::enrichedGOEnriched Gene Ontology terms used as example
- ChIPpeakAnno::myPeakListAn example GRanges object representing a ChIP-seq peak dataset
- ChIPpeakAnno::peaks1An example GRanges object representing a ChIP-seq peak dataset
- ChIPpeakAnno::peaks2An example GRanges object representing a ChIP-seq peak dataset
- ChIPpeakAnno::peaks3An example GRanges object representing a ChIP-seq peak dataset
- ChIPpeakAnno::wgEncodeTfbsV3transcription factor binding site clusters (V3) from ENCODE
- ChIPQC::blacklist_hg19Example data sets for 'ChIPQC' package, each containing a 'ChIPQCexperiment' object, as well as a pre-compiled blacklist for hg19.
- ChIPQC::exampleExpExample data sets for 'ChIPQC' package, each containing a 'ChIPQCexperiment' object, as well as a pre-compiled blacklist for hg19.
- ChIPQC::tamoxifenExample data sets for 'ChIPQC' package, each containing a 'ChIPQCexperiment' object, as well as a pre-compiled blacklist for hg19.
- ChIPseeker::gsminfoInformation Datasets
- ChIPseeker::tagMatrixListInformation Datasets
- ChIPseeker::ucsc_releaseInformation Datasets
- chipseq::cstestA test ChIP-Seq dataset
- ChIPXpress::Oct4ESC_ChIPgenesPredicted Oct4 bound genes in embryonic stem cells (ESC) obtained from analyzing ChIP-seq data
- chopsticks::AsnpsTest data for the snpMatrix package
- chopsticks::AutosomesTest data for the snpMatrix package
- chopsticks::XchromosomeTest data for the snpMatrix package
- chopsticks::XsnpsTest data for the snpMatrix package
- chopsticks::snp.supportData for exercise in use of the snpMatrix package
- chopsticks::snps.10Data for exercise in use of the snpMatrix package
- chopsticks::subject.dataTest data for the snpMatrix package
- chopsticks::subject.supportData for exercise in use of the snpMatrix package
- ChromHeatMap::ALLs.chr22Chromosome 22 subset of ALL data for ALL1/AF4 and E2A/PBX1
- ChromHeatMap::chrdataThe ALLs.chr22 ExpressionSet, reformatted as a ChrStrandData object
- ChromHeatMap::cytobandsCytoband location information
- ChromHeatMap::stainsCytoband display information
- chromPlot::hg_cytoBandIdeocytoBandIdeo human
- chromPlot::hg_gapHuman Gap
- chromPlot::mm10_cytoBandIdeocytoBandIdeo
- chromPlot::mm10_gapGaps
- ChromSCape::CheA3_TF_nTargetsA data.frame with the number of targets of each TF in ChEA3
- ChromSCape::hg38.GeneTSSData.frame of gene TSS - hg38
- ChromSCape::hg38.chromosomesData.frame of chromosome length - hg38
- ChromSCape::hg38.cytoBandData.frame of cytoBandlocation - hg38
- ChromSCape::mm10.GeneTSSData.frame of gene TSS - mm10
- ChromSCape::mm10.chromosomesData.frame of chromosome length - mm10
- ChromSCape::mm10.cytoBandData.frame of cytoBandlocation - mm10
- ChromSCape::scExpA SingleCellExperiment outputed by ChromSCape
- chromstaR::genes_rn4Gene coordinates for rn4
- chromstaR::model.combinedCombined multivariate HMM for demonstration purposes
- chromstaR::model.multivariateMultivariate HMM for demonstration purposes
- chromstaR::model.univariateUnivariate HMM for demonstration purposes
- chromVAR::example_countsexample_counts
- chromVAR::mini_countsmini_counts
- chromVAR::mini_devmini_dev
- chromVAR::mini_ixmini_ix
- cicero::cell_dataMetadata for example cells in cicero_data
- cicero::cicero_dataExample single-cell chromatin accessibility data
- cicero::gene_annotation_sampleExample gene annotation information
- cicero::human.hg19.genomeChromosome lengths from human genome hg19
- CINdex::clin.crcColon cancer clinical dataset
- CINdex::cnvgr.18.autoProbe annotation file for Affymetrix Genome Wide Human SNP Array 6.0
- CINdex::cyto.cin4heatmapCytoband CIN T-test output
- CINdex::cytobands.cinCytoband CIN dataset
- CINdex::geneAnnoCDS gene annotation file
- CINdex::grl.dataOutput of segmentation algorithm
- CINdex::hg18.ucsctrackHuman reference annotation file
- CINdex::snpgr.18.autoProbe annotation file for Affymetrix Genome Wide Human SNP Array 6.0
- circRNAprofiler::ahChainFilesahChainFile
- circRNAprofiler::ahRepeatMaskerahRepeatMasker
- circRNAprofiler::attractSpeciesattractSpecies
- circRNAprofiler::backSplicedJunctionsbackSplicedJunctions
- circRNAprofiler::gtfgtf
- circRNAprofiler::gwasTraitsgwasTraits
- circRNAprofiler::iupaciupac
- circRNAprofiler::memeDBmemeDB
- circRNAprofiler::mergedBSJunctionsmergedBSJunctions
- circRNAprofiler::miRspeciesCodesmiRspeciesCodes
- CiteFuse::CITEseq_exampleA subset of ECCITE-seq data (control)
- CiteFuse::lr_pair_subsetA subset of Ligand Receptor Pairs
- CiteFuse::sce_control_subsetA SingleCellExperiment of ECCITE-seq data
- CiteFuse::sce_ctcl_subsetA SingleCellExperiment of ECCITE-seq data
- ClassifyR::classesAsthma RNA Abundance and Patient Classes
- ClassifyR::clinicalMETABRIC Clinical Data
- ClassifyR::interactorsHuman Reference Interactome
- ClassifyR::measurementsAsthma RNA Abundance and Patient Classes
- cleanUpdTSeq::classifierNaiveBayes classifier
- cleanUpdTSeq::data.NaiveBayesTraining Data
- CleanUpRNAseq::feature_counts_listGC content and lengths of 2000 intergenic regions
- CleanUpRNAseq::gene_GCGC content and lengths of 2000 human genes
- CleanUpRNAseq::intergenic_GCGC content and lengths of 2000 intergenic regions
- CleanUpRNAseq::salmon_quantGC content and lengths of 2000 intergenic regions
- clippda::liverRawDataA dataframe of the protein expression data, peak information and sample information
- clippda::liver_phenoA dataframe of phenotypic information
- clippda::liverdataA dataframe of the protein expression data, peak information, and sample information
- clippda::pheno_urineA dataframe of phenotypic information
- Clomial::Clomial1000Pre-computed results of Clomial.
- Clomial::breastCancerBreast cancer data for clonal decomposition.
- clst::actinoActinomyces data set
- clst::bvseqsBV reference set.
- clst::strepStreptococcus data set.
- clstutils::seqdatAnnotation for the Enterococcus sequence data set.
- clstutils::seqsEnterococcus sequence data set.
- ClustAll::obj_noNA1obj_noNA1: Processed wdbc dataset for testing purposed
- ClustAll::obj_noNA1simplifyobj_noNA1simplify: Processed wdbc dataset for testing purposed
- ClustAll::obj_noNAno1Validationobj_noNAno1Validation: Processed wdbc dataset for testing purposed
- ClustAll::wdbcwdbc: Diagnostic Wisconsin Breast Cancer Database.
- ClustAll::wdbcMIDSwdbcMIDS: Diagnostic Wisconsin Breast Cancer Database with imputed values
- ClustAll::wdbcNAwdbcNA: Diagnostic Wisconsin Breast Cancer Database with missing values
- clusterExperiment::fluidigmColDataSubset of fluidigm data
- clusterExperiment::fluidigmDataSubset of fluidigm data
- clusterExperiment::rsecFluidigmDocumentation of rsecFluidigm object
- clusterExperiment::simCountSimulated data for running examples
- clusterExperiment::simDataSimulated data for running examples
- clusterExperiment::trueClusterSimulated data for running examples
- ClusterJudge::Yeast.GO.assocsGene Ontology attributes associated to Yeast Gene entities
- ClusterJudge::mi.GO.Yeastprecalculated mutual information between Gene Ontology attributes of Yeast genes
- clusterProfiler::DE_GSE8057Datasets gcSample contains a sample of gene clusters.
- clusterProfiler::gcSampleDatasets gcSample contains a sample of gene clusters.
- clusterProfiler::kegg_categoryDatasets gcSample contains a sample of gene clusters.
- clusterProfiler::kegg_speciesDatasets gcSample contains a sample of gene clusters.
- clusterSeq::cD.ratThymusData from female rat thymus tissue taken from the Rat BodyMap project (Yu et al, 2014) and processed by baySeq.
- clusterSeq::ratThymusData from female rat thymus tissue taken from the Rat BodyMap project (Yu et al, 2014).
- ClusterSignificance::mlpMatrixSimulated data used to demonstrate the Mlp method.
- ClusterSignificance::pcpMatrixSimulated data used to demonstrate the Pcp method.
- clustifyr::cbmc_mreference marker matrix from seurat citeseq CBMC tutorial
- clustifyr::cbmc_refreference matrix from seurat citeseq CBMC tutorial
- clustifyr::downrefstable of references stored in clustifyrdata
- clustifyr::human_genes_10xVector of human genes for 10x cellranger pipeline
- clustifyr::mouse_genes_10xVector of mouse genes for 10x cellranger pipeline
- clustifyr::object_loc_lookuplookup table for single cell object structures
- clustifyr::pbmc_markersMarker genes identified by Seurat from single-cell RNA-seq PBMCs.
- clustifyr::pbmc_markers_M3DropMarker genes identified by M3Drop from single-cell RNA-seq PBMCs.
- clustifyr::pbmc_matrix_smallMatrix of single-cell RNA-seq PBMCs.
- clustifyr::pbmc_metaMeta-data for single-cell RNA-seq PBMCs.
- clustifyr::pbmc_vargenesVariable genes identified by Seurat from single-cell RNA-seq PBMCs.
- ClustIRR::CDR3abMock data set of complementarity determining region 3 (CDR3) sequences from the alpha and beta chains of 10,000 T cell receptors
- ClustIRR::mcpasCDR3 sequences and their matching epitopes obtained from McPAS-TCR
- ClustIRR::tcr3dCDR3 sequences and their matching epitopes obtained from TCR3d
- ClustIRR::vdjdbCDR3 sequences and their matching epitopes obtained from VDJdb
- CMA::golubALL/AML dataset of Golub et al. (1999)
- CMA::khanSmall blue round cell tumor dataset of Khan et al. (2001)
- cmapR::cdesc_charAn example table of metadata, as would be parsed from or parse.gctx. Initially all the columns are of type character.
- cmapR::dsAn example of a GCT object with row and column metadata and gene expression values in the matrix.
- cmapR::gene_setAn example collection of gene sets as used in the Lamb 2006 CMap paper.
- cmapR::kd_gctAn example GCT object of knockdown experiments targeting a subset of landmark genes.
- cn.mops::CNVRangesGenomic locations and indices of the simulated CNVs.
- cn.mops::XA simulated data set for CNV detection from NGS data.
- cn.mops::XRangesA simulated data set for CNV detection from NGS data.
- cn.mops::exomeCountsRead counts from exome sequencing for CNV detection
- CNAnorm::CNA CNAnorm object with information about most abundant ploidy states, obtained from data LS041.
- CNAnorm::LS041Mapped reads in tumor and matched blood for patient LS041
- CNAnorm::gParAn object with the default graphical parameters
- CNAnorm::hg19_hs_ideogrAn object with the ideogram information for homo sapiens - hg19
- CNEr::CNEDanRer10Hg38CNEHg38DanRer10 and CNEDanRer10Hg38 dataset
- CNEr::CNEHg38DanRer10CNEHg38DanRer10 and CNEDanRer10Hg38 dataset
- CNEr::axisTrackExample data for plotting annotation.
- CNEr::cneFinalListDanRer10Hg38cneFinalListDanRer10Hg38 dataset
- CNEr::cpgIslandsExample data for plotting annotation.
- CNEr::grangesPairsForDotplotgrangesPairsForDotplot
- CNEr::refGenesExample data for plotting annotation.
- CNORdt::CNOlistPBToy data
- CNORdt::modelPBmodelPB
- CNORfeeder::PPINigraphProtein-protein interaction netwrok
- CNORfeeder::UniprotIDdreamUniprot identifiers for proteins in DreamModel
- CNORfeeder::cnolistCNOlist
- CNORfeeder::cnolistCNOlist
- CNORfeeder::databaseOmniPath PPI
- CNORfeeder::feederObjectFeeder Object
- CNORfeeder::indicesMis-fit indices
- CNORfeeder::integratedModelIntegrated Model
- CNORfeeder::modelPrior Knowledge Network
- CNORfeeder::modelPrior Knowledge Network
- CNORfeeder::simDataCNORode simuation data
- CNORode::cnodataA cnodata from CellNoptR
- CNORode::cnolistA cnolist from CellNoptR
- CNORode::cnolistCNORodeExampleA cnolist from CellNoptR
- CNORode::indicesIndices that relate cnolist to model
- CNORode::modelA model from CellNoptR
- CNORode::pknmodelA pknmodel from CellNoptR
- CNORode::pknmodelA pknmodel from CellNoptR
- CNTools::geneInfomethod that convert segment data into reduced segment matrix
- CNTools::sampleDataClass "CNSeg" contains the output of DNACopy segmentation data that can be operated on by the associated methods
- CNViz::gene_dataGene data for vignette example
- CNViz::meta_dataMetadata for vignette example
- CNViz::probe_dataProbe data for vignette example
- CNViz::segment_dataSegment data for vignette example
- CNViz::variant_dataVariant data for vignette example
- CNVPanelizer::referenceReadCountsReference sample data
- CNVPanelizer::sampleReadCountsTest sample data
- CNVrd2::ccl3l1dataData of CCL3L1 gene (The 1000 Genomes Project)
- CNVrd2::copynumberGroupsMXL population data (The 1000 Genomes Project)
- CNVrd2::objectCNVrd2MXL population data (The 1000 Genomes Project)
- CNVrd2::resultSegmentMXL population data (The 1000 Genomes Project)
- COCOA::atf3_chr1Atf3 binding regions.
- COCOA::brcaATACCoord1A GRanges object with coordinates for select BRCA ATAC-seq peak regions from chr1.
- COCOA::brcaATACData1A matrix with ATAC-seq counts in select peak regions from chromosome 1 for 37 patients.
- COCOA::brcaMCoord1A GRanges object with genomic coordinates for cytosines from chr1 for the package's built-in DNA methylation data
- COCOA::brcaMetadataA data.frame with patient metadata for breast cancer patients.
- COCOA::brcaMethylData1A matrix with DNA methylation levels from some CpGs on chromosome 1
- COCOA::brcaPCScoresA matrix with principal component scores for PCs 1-4 for four breast cancer patients.
- COCOA::brcaPCScores657A data.frame with principal component scores for PCs 1-4 for 657 breast cancer patients as well as a column with estrogen receptor status.
- COCOA::esr1_chr1Estrogen receptor alpha binding regions.
- COCOA::gata3_chr1Gata3 binding regions.
- COCOA::nrf1_chr1Nrf1 binding regions.
- COCOA::rsScoresExample COCOA Results (made up)
- codelink::codelink.exampleDataset of class 'Codelink'
- codelink::codsetDataset of class 'CodelinkSet'
- CODEX::bambedObjDemoDemo data pre-stored for bambedObj.
- CODEX::coverageObjDemoDemo data pre-stored for coverageObj.
- CODEX::gcDemoDemo data pre-stored for GC content.
- CODEX::mappDemoDemo data pre-stored for mappability.
- CODEX::mapp_refPosition reference for pre-computed mappability results.
- CODEX::mappabilityPre-computed mappabilities
- CODEX::normObjDemoDemo data pre-stored for normObj.
- CODEX::qcObjDemoDemo data pre-stored for qcObj.
- CoGAPS::GIST.data_frameGIST gene expression data from Ochs et al. (2009)
- CoGAPS::GIST.matrixGIST gene expression data from Ochs et al. (2009)
- CoGAPS::GIST.resultCoGAPS result from running on GIST dataset
- CoGAPS::GIST.uncertaintyGIST gene expression uncertainty matrix from Ochs et al. (2009)
- CoGAPS::modsimdataToy example to run CoGAPS on.
- CoGAPS::modsimresultResult of applying CoGAPS on the Toy example.
- cogena::AllGeneSymbolsAll the gene symbols
- cogena::DEexprsgene expression of DEG
- cogena::sampleLabellabel of samples
- cogeqc::batch_summaryBUSCO summary output for batch mode
- cogeqc::interpro_athIntepro annotation for Arabidopsis thaliana's genes
- cogeqc::interpro_bolIntepro annotation for Brassica oleraceae's genes
- cogeqc::ogOrthogroups between Arabidopsis thaliana and Brassica oleraceae
- cogeqc::synnetSynteny network for Brassica oleraceae, B. napus, and B. rapa
- cogeqc::treeSpecies tree for model species
- Cogito::MurEpi.ChIP.smallExample data set: Murine ChIP-seq data of GEO GSE77004
- Cogito::MurEpi.RNA.smallExample data set: Murine RNA-seq RPKM values of GSE77004
- Cogito::MurEpi.RRBS.smallExample data set: Murine methylation status data set of GSE77004
- coGPS::CNV_classlab_matchedSample Data for coGPS
- coGPS::CNV_exprs_matchedSample Data for coGPS
- coGPS::Exon_classlab_matchedSample Data for coGPS
- coGPS::Exon_exprs_matchedSample Data for coGPS
- coGPS::Hs.gmtl.c1Sample Data for coGPS
- coGPS::Methy_classlab_matchedSample Data for coGPS
- coGPS::Methy_exprs_matchedSample Data for coGPS
- cola::cola_rlExample ConsensusPartitionList object
- cola::golub_colaExample ConsensusPartitionList object from Golub dataset
- cola::golub_cola_dsExample DownSamplingConsensusPartition object from Golub dataset
- cola::golub_cola_rhExample HierarchicalPartition object from Golub dataset
- comapr::coCountRangedSummarizedExperiment object containing the crossover counts across samples for the list of SNP marker intervals
- comapr::parents_genoParents' genotype for F1 samples in 'snp_geno'
- comapr::snp_genoMarkers by genotype results for a group of samples
- comapr::snp_geno_grMarkers by genotype results for a group of samples
- comapr::twoSamplesRangedSummarizedExperiment object containing the Viterbi states SNP markers for samples from two groups. 'colData(twoSamples)' contains the sample group factor.
- combi::zhangMetaboMetabolomes of mice that underwent Pulsed Antibiotic Treatment (PAT) and controls
- combi::zhangMetavarsBaseline sample variables of PAT and control mice
- combi::zhangMicrobioMicrobiomes of mice that underwent Pulsed Antibiotic Treatment (PAT) and controls
- coMET::DNaseI_RoadMapSingleData sets
- coMET::DupTrackData sets
- coMET::DupTrackData sets
- coMET::OtherRegulatoryRegionsTrackAllData sets
- coMET::OtherRegulatoryRegionsTrackSingleData sets
- coMET::PancreasIGData sets
- coMET::PancreasIGtrackData sets
- coMET::PancreasimprintedIGData sets
- coMET::PancreasimprintedIGtrackData sets
- coMET::RegulatoryEvidenceBiomartTrackAllData sets
- coMET::RegulatoryEvidenceBiomartTrackMultipleData sets
- coMET::RegulatoryEvidenceBiomartTrackSingleData sets
- coMET::RegulatoryFeaturesBiomartTrackAllData sets
- coMET::RegulatoryFeaturesBiomartTrackMultipleData sets
- coMET::RegulatoryFeaturesBiomartTrackSingleData sets
- coMET::RegulatorySegmentsBiomartTrackAllData sets
- coMET::RegulatorySegmentsBiomartTrackMultipleData sets
- coMET::RegulatorySegmentsBiomartTrackSingleData sets
- coMET::StomachIGData sets
- coMET::StomachIGtrackData sets
- coMET::allIGData sets
- coMET::allIGtrackData sets
- coMET::allimprintedIGData sets
- coMET::allimprintedIGtrackData sets
- coMET::bindMotifsBiomartTrackAllData sets
- coMET::bindMotifsBiomartTrackAllData sets
- coMET::bindMotifsBiomartTrackAllData sets
- coMET::bindMotifsBiomartTrackDoubleData sets
- coMET::bindMotifsBiomartTrackMultipleData sets
- coMET::bindMotifsBiomartTrackMultipleData sets
- coMET::bindMotifsBiomartTrackSingleData sets
- coMET::bindMotifsBiomartTrackSingleData sets
- coMET::bindMotifsBiomartTrackSingleData sets
- coMET::chipTFtrackData sets
- coMET::chipTFtrackData sets
- coMET::chromHMM_RoadMapAllData sets
- coMET::chromHMM_RoadMapAllE063Data sets
- coMET::chromHMM_RoadMapMultipleData sets
- coMET::chromHMM_RoadMapSingleData sets
- coMET::chromatinHMMRoadMapAllData sets
- coMET::chromatinHMMRoadMapMultipleData sets
- coMET::chromatinHMMRoadMapSingleData sets
- coMET::chromhmmNoPatternData sets
- coMET::chromhmmPatternData sets
- coMET::chromhmmtrackoneData sets
- coMET::clinCNVData sets
- coMET::clinVariantData sets
- coMET::coreilVariantData sets
- coMET::coreilVariantData sets
- coMET::cosmicVariantData sets
- coMET::cpgIstrackData sets
- coMET::cpgIstrackData sets
- coMET::dgfootprints_RoadMapSingleData sets
- coMET::dnasetrackData sets
- coMET::dyaRMData sets
- coMET::dyaRMtrackData sets
- coMET::eGTexTrackSNPData sets
- coMET::eGTexTrackallData sets
- coMET::eQTLTrackAllData sets
- coMET::eQTLTrackAllData sets
- coMET::eQTLTrackMultipleData sets
- coMET::eQTLTrackMultipleData sets
- coMET::eQTLTrackSingleData sets
- coMET::eQTLTrackSingleData sets
- coMET::enhFANTOMtrackData sets
- coMET::enhRMData sets
- coMET::enhRMtrackData sets
- coMET::gadtrackData sets
- coMET::gctrackData sets
- coMET::gctrackData sets
- coMET::geneNameEnsemblData sets
- coMET::geneNameEnsemblData sets
- coMET::geneRtrackData sets
- coMET::geneRtrackData sets
- coMET::genesUcsctrackData sets
- coMET::genesUcsctrackData sets
- coMET::genesUcsctrackData sets
- coMET::genetrackData sets
- coMET::genetrackData sets
- coMET::genetrackData sets
- coMET::genetrackData sets
- coMET::grtrackData sets
- coMET::grtrackData sets
- coMET::gwastrackData sets
- coMET::histonalltrackData sets
- coMET::histoneonetrackData sets
- coMET::imprintedGenesGTExData sets
- coMET::interestgenesENSMBLtrackData sets
- coMET::interestgenesENSMBLtrackData sets
- coMET::interesttransENSMBLtrackData sets
- coMET::interesttransENSMBLtrackData sets
- coMET::iscatrackData sets
- coMET::iscatrackData sets
- coMET::matrix_HiC_RaoData sets
- coMET::metQTLTrackAllData sets
- coMET::metQTLTrackMultipleData sets
- coMET::metQTLTrackSingleData sets
- coMET::metQTLTrackSingleData sets
- coMET::miRNATargetRegionsBiomartTrackData sets
- coMET::miRNATargetRegionsBiomartTrackData sets
- coMET::otherRegulatoryRegionsTrackAllData sets
- coMET::otherRegulatoryRegionsTrackSingleData sets
- coMET::promRMtrackData sets
- coMET::promRMtrackE063Data sets
- coMET::psiGTexData sets
- coMET::psiGTexTrackSNPData sets
- coMET::psiGTexTrackallData sets
- coMET::regulationENSEMBLtrackData sets
- coMET::regulatoryEvidenceBiomartTrackAllData sets
- coMET::regulatoryEvidenceBiomartTrackMultipleData sets
- coMET::regulatoryEvidenceBiomartTrackSingleData sets
- coMET::regulatoryFeaturesBiomartTrackAllData sets
- coMET::regulatoryFeaturesBiomartTrackMultipleData sets
- coMET::regulatoryFeaturesBiomartTrackSingleData sets
- coMET::regulatorySegmentsBiomartTrackAllData sets
- coMET::regulatorySegmentsBiomartTrackMultipleData sets
- coMET::regulatorySegmentsBiomartTrackSingleData sets
- coMET::rmtrackData sets
- coMET::snpUCSCtrackData sets
- coMET::snptrackData sets
- coMET::snptrackData sets
- coMET::snptrackData sets
- coMET::strutrackData sets
- coMET::strutrackData sets
- coMET::tfbsFANTOMtrackData sets
- coMET::transENSMBLtrackData sets
- coMET::xenogenestrackData sets
- coMET::xenogenestrackData sets
- coMethDMR::betaMatrix_ex1Alzheimer's Prefrontal Cortex (PFC) Methylation Data
- coMethDMR::betaMatrix_ex2Alzheimer's Prefrontal Cortex (PFC) Methylation Data
- coMethDMR::betaMatrix_ex3Alzheimer's Prefrontal Cortex (PFC) Methylation Data
- coMethDMR::betaMatrix_ex4Alzheimer's Prefrontal Cortex (PFC) Methylation Data
- coMethDMR::betasChr22_dfPrefrontal Cortex (PFC) Methylation Data from Alzheimer's Disease subjects
- coMethDMR::pheno_dfExample phenotype data file from Prefrontal Cortex (PFC) Methylation Data of Alzheimer's Disease subjects
- COMPASS::CCSimulated COMPASSContainer
- COMPASS::CRSimulated COMPASS fit
- compSPOT::compSPOT_example_mutationsSingle Nucleotide Variants and Patient Features in Lung Cancer Patients
- compSPOT::compSPOT_example_regionsGenomic Coordinates of Regions of Interest
- condiments::toy_datasetA toy dataset used in the vignette and in the examples
- CONFESS::ResultsResults
- CONFESS::cluclu
- CONFESS::estimatesestimates
- CONFESS::estimates.2estimates.2
- CONFESS::filesfiles
- CONFESS::step1step1
- CONFESS::step2step2
- CONFESS::step2.1step2.1
- CONFESS::step3step3
- CONFESS::step3.1step3.1
- CONFESS::step4step4
- CONFESS::steps2_4steps2_4
- consensus::AgilentAgilent microarray gene expression data
- consensus::HuexAffymetrix Huex gene expression data
- consensus::RNASeqRNA-Seq gene expression data
- consensus::U133AAffymetrix U133A gene expression data
- consensusOV::GSE14764.esetSample ExpressionSet from MetaGxOvarian
- consensusSeekeR::A549_CTCF_MYJ_NarrowPeaks_partialSites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)
- consensusSeekeR::A549_CTCF_MYJ_Peaks_partialSites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)
- consensusSeekeR::A549_CTCF_MYN_NarrowPeaks_partialSites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)
- consensusSeekeR::A549_CTCF_MYN_Peaks_partialSites with the greatest evidence of transcription factor binding for the CTCF transcription factor (for demonstration purpose)
- consensusSeekeR::A549_FOSL2_01_NarrowPeaks_partialGenomic regions with the greatest evidence of transcription factor binding for the FOSL2 transcription factor (for demonstration purpose)
- consensusSeekeR::A549_FOSL2_01_Peaks_partialSites with the greatest evidence of transcription factor binding for the FOSL2 transcription factor (for demonstration purpose)
- consensusSeekeR::A549_FOXA1_01_NarrowPeaks_partialGenomic regions with the greatest evidence of transcription factor binding for the FOXA1 transcription factor (for demonstration purpose)
- consensusSeekeR::A549_FOXA1_01_Peaks_partialSites with the greatest evidence of transcription factor binding for the FOXA1 transcription factor (for demonstration purpose)
- consensusSeekeR::A549_NR3C1_CFQ_NarrowPeaks_partialRanges with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFQ). For demonstration purpose.
- consensusSeekeR::A549_NR3C1_CFQ_Peaks_partialSites with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFQ). For demonstration purpose.
- consensusSeekeR::A549_NR3C1_CFR_NarrowPeaks_partialRanges with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFR). For demonstration purpose.
- consensusSeekeR::A549_NR3C1_CFR_Peaks_partialSites with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFR). For demonstration purpose.
- consensusSeekeR::A549_NR3C1_CFS_NarrowPeaks_partialRanges with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFS). For demonstration purpose.
- consensusSeekeR::A549_NR3C1_CFS_Peaks_partialSites with the greatest evidence of transcription factor binding for the NR3C1 transcription factor from ENCODE (DDC accession: ENCFF002CFS). For demonstration purpose.
- consensusSeekeR::NOrMAL_nucleosome_positionsNucleosome positions detected by the NOrMAL software using syntetic reads generated using a normal distribution. For demonstration purpose.
- consensusSeekeR::NOrMAL_nucleosome_rangesRanges associated to nucleosomes detected by the NOrMAL software using syntetic reads generated using a normal distribution. For demonstration purpose.
- consensusSeekeR::NucPosSimulator_nucleosome_positionsNucleosome positions detected by the NucPosSimulator software using syntetic reads generated using a normal distribution. For demonstration purpose.
- consensusSeekeR::NucPosSimulator_nucleosome_rangesRanges associated to nucleosomes detected by the NucPosSimulator software using syntetic reads generated using a normal distribution. For demonstration purpose.
- consensusSeekeR::PING_nucleosome_positionsNucleosome positions detected by the PING software using syntetic reads generated using a normal distribution. For demonstration purpose.
- consensusSeekeR::PING_nucleosome_rangesRanges associated to nucleosomes detected by the PING software using syntetic reads generated using a normal distribution. For demonstration purpose.
- consICA::samples_dataSamples of gene expression
- conumee::detail_regionsdetail_regions
- conumee::exclude_regionsexclude_regions
- conumee::tcgaBRCA.sentrix2nametcgaBRCA.sentrix2name
- coRdon::HD59Codon usage in healthy human gut microbiome.
- coRdon::HD59_KOCodon usage based KO enrichment analysis results from the healthy human gut microbiome. For more information, see '?HD59'.
- coRdon::HD59_PATHWAYSCodon usage based KEGG Pathway enrichment analysis results from a healthy human gut microbiome. For more information, see '?HD59'.
- coRdon::LD94Codon usage in human gut microbiome in liver cirrhosis.
- coRdon::LD94_KOCodon usage based KO enrichment analysis results from an gut microbiome of an individual with liver cirrhosis. For more information, see '?LD94'.
- coRdon::LD94_PATHWAYSCodon usage based KEGG Pathway enrichment analysis results from an gut microbiome of an individual with liver cirrhosis. For more information, see '?LD94'.
- CoreGx::clevelandSmall_cSetCleaveland_mut RadioSet subsetted and cast as CoreSet
- CoreGx::exampleDataMapperExample LongTableDataMapper
- CoreGx::merckLongTableMerck Drug Combination Data LongTable
- CoreGx::nci_TRE_smallNCI-ALMANAC Drug Combination Data TreatmentResponseExperiment Subset
- Cormotif::simu2_compgroupExample dataset for Cormotif
- Cormotif::simu2_groupidExample dataset for Cormotif
- Cormotif::simudata2Example dataset for Cormotif
- coseq::fietzRNA-seq data from the mouse neocortex in Fietz et al. (2012)
- cosmosR::HMDB_mapper_vecToy Input Transcription Data Set
- cosmosR::meta_networkMeta Prior Knowledge Network
- cosmosR::toy_RNAToy Input Transcription Data Set
- cosmosR::toy_metabolic_inputToy Metabolic Input Data
- cosmosR::toy_networkToy Input Network
- cosmosR::toy_signaling_inputToy Signaling Input
- COTAN::ERCCrawData-sets
- COTAN::raw.datasetData-sets
- COTAN::test.datasetData-sets
- COTAN::test.dataset.clusters1Data-sets
- COTAN::test.dataset.clusters2Data-sets
- COTAN::vignette.merge.clustersData-sets
- COTAN::vignette.split.clustersData-sets
- countsimQC::countsimExampleExample list with three count data sets
- countsimQC::countsimExample_dfmatExample list with three count data sets in different formats
- CoverageView::DF_H3K36me3Example of a coverage matrix using the ChIP-seq data for the H3K36me3 histone modification experiment
- CoverageView::DF_H3K36me3_controlExample of a coverage matrix using the control replicate for the ChIP-seq data for the H3K36me3 histone modification experiment
- CoverageView::DF_H3K4me3Example of a coverage matrix using the ChIP-seq data for the H3K4me3 histone modification experiment
- CoverageView::DF_H3K4me3_ctlExample of a coverage matrix using the control replicate for the ChIP-seq data for the H3K4me3 histone modification experiment
- CoverageView::DF_H3K4me3_nopeaks_ratiosExample of a matrix with the ratio of the coverages using the ChIP-seq data for the H3K4me3 histone modification experiment
- CoverageView::FoxA1_chr19Example of a coverage matrix using the ChIP-seq data for the FoxA1 transcription factor experiment
- covRNA::BacaThe Baca dataset
- cpvSNP::geneSetAnalysisData to run gene set analysis methods
- cqn::montgomery.subsetMongtomery RNA-seq data.
- cqn::sizeFactors.subsetMongtomery RNA-seq data.
- cqn::uCovarMongtomery RNA-seq data.
- CRISPRball::depmap_22q1_TPMDepMap expression data
- CRISPRball::depmap_22q1_cnDepMap copy number data
- CRISPRball::depmap_22q1_crisprDepMap CRISPR screen data
- CRISPRball::depmap_22q1_crispr_rnaiDepMap CRISPR & RNAi screen data
- CRISPRball::depmap_22q1_rnaiDepMap RNAi screen data
- crisprBase::AsCas12aAsCas12a CrisprNuclease object
- crisprBase::BE4maxBE4max BaseEditor object
- crisprBase::CasRxCasRx CrisprNuclease object
- crisprBase::CsmCsm CrisprNuclease object
- crisprBase::MAD7MAD7 CrisprNuclease object
- crisprBase::SaCas9SaCas9 CrisprNuclease object
- crisprBase::SpCas9SpCas9 CrisprNuclease object
- crisprBase::SpGCas9SpGCas9 CrisprNuclease object
- crisprBase::enAsCas12aenAsCas12a CrisprNuclease object
- crisprBase::restrictionEnzymesList of Nuclease objects representing common restriction enzymes
- crisprDesign::grListExampleExample of a TxDb object converted to a GRangesList
- crisprDesign::grRepeatsExampleExample of a GRanges object containing repeat elements
- crisprDesign::guideSetExampleExample of a GuideSet object storing gRNA sequences targeting the CDS of IQSEC3
- crisprDesign::guideSetExampleFullAnnotationExample of a fully-annotated GuideSet object storing gRNA sequences targeting the CDS of IQSEC3
- crisprDesign::guideSetExampleWithAlignmentsExample of a GuideSet object storing gRNA sequences targeting the CDS of IQSEC3 with off-target alignments.
- crisprDesign::tssObjectExampleExample of a GRanges object containing TSS coordinates
- crisprScore::scoringMethodsInfodata.frame detailing available scoring methods
- crisprScore::sgrnaExampleCrispraExample CRISPRa gRNAs data.frame for the getCrispraiScores function
- crisprScore::sgrnaExampleCrispriExample CRISPRi gRNAs data.frame for the getCrispraiScores function
- crisprScore::tssExampleCrispraExample TSS data.frame for the getCrispraiScores function
- crisprScore::tssExampleCrispriExample TSS data.frame for the getCrispraiScores function
- crisprShiny::guideSetExample_basicExample of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS
- crisprShiny::guideSetExample_krasExample of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS
- crisprShiny::guideSetExample_kras_beExample of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS
- crisprShiny::guideSetExample_ntcsExample of a GuideSet object storing gRNA sequences targeting the CDS of the human gene KRAS and NTCs
- crisprShiny::tooltipAnnotationList of tooltip annotations
- crisprShiny::tss_krasExample of a 'GenomicRanges' object storing annotated TSS ranges for the human gene KRAS
- crisprShiny::txdb_krasExample of a 'CompressedGenomicRangesList' object storing annotated ranges for the human gene KRAS
- CrispRVariants::golVariant sequences from golden clutch 1 (Burger et al)
- crisprViz::cageCAGE peak annotation from AnnotationHub
- crisprViz::cas12aGuideSetExample GuideSet targeting the human LTN1 gene.
- crisprViz::cas9GuideSetExample GuideSet targeting the human LTN1 gene.
- crisprViz::dnaseDNase I hypersensitive site annotation from AnnotationHub
- crisprViz::gpr21GeneModelCompressedGRangesList describing the human GPR21 gene.
- crisprViz::gpr21GuideSetExample GuideSet targeting the human GPR21 gene.
- crisprViz::krasGeneModelCompressedGRangesList describing the human KRAS gene.
- crisprViz::krasGuideSetExample GuideSet targeting the human KRAS gene.
- crisprViz::ltn1GeneModelCompressedGRangesList describing the human LTN1 gene.
- crisprViz::mmp7GeneModelCompressedGRangesList describing the human MMP7 gene.
- crisprViz::mmp7GuideSetExample GuideSet targeting the human MMP7 gene.
- crisprViz::repeatsSubset of repeat elements for hg38.
- crlmm::cnSetExampleObject of class 'CNSet'
- crlmm::cnSetExample2Object of class 'CNSet'
- crossmeta::gs.namesMap between KEGG pathway numbers and names.
- crossmeta::gslistKEGG human pathway genes.
- CSAR::TAIR8_genes_testPartial dataset of a ChIP-seq experiment
- CSAR::controlSEP3_testPartial dataset of a ChIP-seq experiment
- CSAR::sampleSEP3_testPartial dataset of a ChIP-seq experiment
- csdR::normal_expressionSample expression matrices for CSD
- csdR::sick_expressionSample expression matrices for CSD
- CTDquerier::gala'CTDdata' for ilustrative purpouses
- cTRAP::ENCODEmetadataENCODE metadata sample
- cTRAP::cmapMetadataCMap metadata
- cTRAP::cmapPerturbationsCompoundsCMap perturbations sample for small molecules
- cTRAP::cmapPerturbationsKDCMap perturbations sample for knockdown experiments
- cTRAP::countsGene expression data sample
- cTRAP::diffExprStatDifferential expression's t-statistics sample
- CTSV::CTSVexample_dataA simulated data set
- cummeRbund::PINK1PINK1
- cummeRbund::sampleGeneSetsampleGeneSet
- cummeRbund::sampleIDssampleIDs
- cypress::ASD_propSimFromData example raw input data
- cypress::GSE60424PowerPower calculation results from immune-related disease (IAD) study (GSE60424)
- cypress::GSE60424_paramSimulation parameters estimated from immune-related disease (IAD) study (GSE60424)
- cypress::asd_nopropPowerPower calculation results From ASD data
- cypress::asd_noprop_paramSimulation parameters estimated from ASD study
- cypress::ibd_propPowerPower calculation results from pediatric inflammatory bowel disease (IBD) study (GSE57945)
- cypress::ibd_prop_paramSimulation parameters estimated from pediatric inflammatory bowel disease (IBD) study (GSE57945)
- cytoKernel::cytoHDBMWExample of processed dimensionally reduced flow cytometry (marker median intensities) Bodenmiller_BCR_XL_flowSet() expression dataset from HDCytoData Bioconductor data package.
- cytomapper::pancreasImagesExample CytoImageList object of image files
- cytomapper::pancreasMasksExample CytoImageList object of segmentation masks
- cytomapper::pancreasSCEExample SingleCellExperiment object
- cytoMEM::MEM_matrixMEM matrix
- cytoMEM::MEM_valuesMEM values
- cytoMEM::PBMCNormal Human Peripheral Blood Mononuclear Cells (PBMCs)
- CytoPipeline::OMIP021SamplesOMIP021Samples dataset
- dada2::errBalancedFAn empirical error matrix.
- dada2::errBalancedRAn empirical error matrix.
- dada2::tperr1An empirical error matrix.
- dagLogo::ecoli.proteomeAn object of 'Proteome-class' representing the _Escherichia coli_ proteome.
- dagLogo::proteome.exampleAn object of 'Proteome-class' representing the subset of _Drosophila melanogaster_ proteome.
- dagLogo::seq.exampleAn object of 'dagPeptides-class' representing acetylated lysine-containing peptides.
- daMA::cinfoVector indexing the matrix cmat
- daMA::cinfoB.ABVector indexing the matrix cmatB.AB
- daMA::cmatContrast matrix describing the experimental questions
- daMA::cmatB.ABContrast matrix describing the experimental questions
- daMA::data.3x23x2 microarray data
- daMA::designs.basicBasic designs for two-colour factorial 3 x 2 microarray data
- daMA::designs.compositeComposite designs for two-colour factorial 3 x 2 microarray data
- daMA::id.3x2A vector of length 30012 containing numeric identifiers of the genes from the microarray dataset data.3x2.
- DAMEfinder::extractbams_outputextract_bams() output.
- DAMEfinder::readtuples_outputread_tuples() output.
- DaMiRseq::SEExample gene-expression dataset for DaMiRseq package
- DaMiRseq::SEtest_normA sample dataset with a normalized count matrix for "testthat" functions.
- DaMiRseq::data_minExample gene-expression dataset for DaMiRseq package
- DaMiRseq::data_normA dataset with a normalized matrix to test several DaMiRseq functions: sample data are a subset of Genotype-Tissue Expression (GTEx) RNA-Seq database (dbGap Study Accession: phs000424.v6.p1)
- DaMiRseq::data_reducedExample gene-expression dataset for DaMiRseq package
- DaMiRseq::data_reliefExample ranking dataset for DaMiRseq package
- DaMiRseq::dfExample gene-expression dataset for DaMiRseq package
- DaMiRseq::selected_featuresExample gene-expression dataset for DaMiRseq package
- DaMiRseq::svExample Surrogate Variables dataset for DaMiRseq package
- Damsel::dros_countsExample Drosophila DamID counts
- dar::metaHIV_phyPhyloseq object from metaHIV project
- dar::test_prep_recPrepRecipe for metaHIV_phy data
- dar::test_recRecipe for metaHIV_phy data
- DART::dataDARTExample data for DART package
- dcanr::sim102Simulated expression data with knock-outs
- DCATS::Haber2017Count matrices of intestinal epithelial scRNA-seq data from three conditions
- DCATS::Kang2017Count matrices of 8 pooled lupus patient samples within two conditions
- DCATS::Ren2021Count matrix and metadata of a large COVID-19 scRNA-seq data cohort.
- DCATS::simulationSimulated dataset with two conditions
- dce::df_pathway_statisticsBiological pathway information.
- dcGSA::dcGSAtestdcGSA test data
- dearseq::PBT_gmtPBT gene sets related to kidney transplant
- dearseq::baduel_gmtSmall portion of RNA-seq data from plant physiology study.
- dearseq::designSmall portion of RNA-seq data from plant physiology study.
- dearseq::expr_norm_corrSmall portion of RNA-seq data from plant physiology study.
- debCAM::ratMix3Gene expression data downsampled from GSE19380
- DECIPHER::BLOSUMBLOSUM Amino Acid Substitution Matrices
- DECIPHER::HEC_MI1Mutual Information for Protein Secondary Structure Prediction
- DECIPHER::HEC_MI2Mutual Information for Protein Secondary Structure Prediction
- DECIPHER::MIQSMIQS Amino Acid Substitution Matrix
- DECIPHER::MMLSUMMMLSUM Amino Acid Substitution Matrices
- DECIPHER::NonCodingRNA_ArchaeaNonCoding Models for Common Non-Coding RNA Families
- DECIPHER::NonCodingRNA_BacteriaNonCoding Models for Common Non-Coding RNA Families
- DECIPHER::NonCodingRNA_EukaryaNonCoding Models for Common Non-Coding RNA Families
- DECIPHER::PAMPAM Amino Acid Substitution Matrices
- DECIPHER::PFASUMPFASUM Amino Acid Substitution Matrices
- DECIPHER::RESTRICTION_ENZYMESCommon Restriction Enzyme's Cut Sites
- DECIPHER::TrainingSet_16STraining Set for Classification of 16S rRNA Gene Sequences
- DECIPHER::deltaGrulesFree Energy of Hybridization of Probe/Target Quadruplets on Microarrays
- DECIPHER::deltaGrulesRNAPseudoenergy Parameters for RNA Quadruplets
- DECIPHER::deltaHrulesChange in Enthalpy of Hybridization of DNA/DNA Quadruplets in Solution
- DECIPHER::deltaHrulesRNAChange in Enthalpy of Hybridization of RNA/RNA Quadruplets in Solution
- DECIPHER::deltaSrulesChange in Entropy of Hybridization of DNA/DNA Quadruplets in Solution
- DECIPHER::deltaSrulesRNAChange in Entropy of Hybridization of RNA/RNA Quadruplets in Solution
- DeconRNASeq::datasetsdata objects for liver and kidney mixing samples
- DeconRNASeq::datasetsdata objects for liver and kidney mixing samples
- DeconRNASeq::fractionmixing fractions for multi-tissues mixing samples
- DeconRNASeq::proportionsproportions for liver and kidney mixing samples
- DeconRNASeq::proportionsproportions for liver and kidney mixing samples
- DeconRNASeq::signaturesdata objects for liver and kidney pure samples
- DeconRNASeq::signaturesdata objects for liver and kidney pure samples
- DeconRNASeq::x.datadata objects for multi-tissues mixing samples
- DeconRNASeq::x.signaturedata objects for multi-tissues pure samples
- DeconRNASeq::x.signature.filteredfiltered signatures for multi-tissues pure samples
- DeconRNASeq::x.signature.filtered.optimalselected signatures from multi-tissues pure samples
- deconvR::HumanCellTypeMethAtlasThe comprehensive human methylome reference atlas
- deconvR::IlluminaMethEpicB5ProbeIDsA dataset Illumina probe IDs of 400000 genomic loci (identified using the “seqnames”, “ranges”, and “strand” values).
- DeepPINCS::SARS_CoV2_3CL_ProteaseAmino Acid Sequence for the SARS coronavirus 3C-like Protease
- DeepPINCS::antiviral_drugList of antiviral drugs with SMILES strings
- DeepPINCS::example_bioassayExample Data for PubChem AID1706 bioassay
- DeepPINCS::example_cciExample Data for Chemical-Chemical Interactions
- DeepPINCS::example_chemExample Data for Compounds
- DeepPINCS::example_cpiExample Data for Compound-Protein Interactions
- DeepPINCS::example_pdExample Data for Primer-Dimer
- DeepPINCS::example_ppiExample Data for Protein-Protein Interactions
- DeepPINCS::example_protExample Data for Proteins
- deepSNV::HIVmixExample .bam data and true SNVs.
- deepSNV::RCCExample RCC data
- deepSNV::countsExample count table
- deepSNV::phiXExample phiX data
- deepSNV::piExample prior
- deepSNV::trueSNVsExample .bam data and true SNVs.
- DeepTarget::OntargetMAn object containing a small part of the data from the Cancer Dependency Map (depmap.org) to demonstrate in DeepTarget pipeline
- DegCre::DexNR3C1DegCre input data for examples.
- DegNorm::coverage_res_chr21Example CoverageClass data
- DegNorm::res_DegNorm_chr21Example DegNormClass data
- DEGraph::annLoi2008Annotation data used in the DEGraph package vignette
- DEGraph::classLoi2008Tamoxifen treatment resistance status data used in the DEGraph package vignette
- DEGraph::exprLoi2008Gene expression data used in the DEGraph package vignette
- DEGraph::grListKEGGKEGG networks used in the DEGraph package vignette
- DEGreport::geneInfodata.frame with chromose information for each gene
- DEGreport::humanGenderDGEList object for DE genes betwen Male and Females
- DelayedTensor::human_mid_brainMatrix object of human mid brain data
- DelayedTensor::mouse_mid_brainMatrix object of mouse mid brain data
- deltaCaptureC::bigBinSizeBig bin size
- deltaCaptureC::binnedDeltaPlotPlot of Binned Delta Counts
- deltaCaptureC::binnedDeltaSEBinned difference of mean capture-C counts between EScells and Neurons
- deltaCaptureC::binnedSummarizedExperimentBinned Capture-C counts of EScells and Neurons
- deltaCaptureC::deltaSEDifference of mean capture-C counts between EScells and Neurons
- deltaCaptureC::miniDeltaSEDifference of mean capture-C counts between EScells and Neurons
- deltaCaptureC::miniSECapture-C counts of EScells and Neurons
- deltaCaptureC::miniSEDFCapture-C counts of EScells and Neurons
- deltaCaptureC::numPermutationsNumber of permutations used in example permutation testing.
- deltaCaptureC::pValueP-value
- deltaCaptureC::plotTitleTitle for delta capture-C plot
- deltaCaptureC::regionOfInterestRegion of interest surrounding the viewpoint
- deltaCaptureC::significanceTypeType for testing significance
- deltaCaptureC::significantRegionsRegions of significant remodeling in example data
- deltaCaptureC::significantRegionsPlotA plot of the significant regions in the sample data.
- deltaCaptureC::smallBinSizeSmall Bin Size
- deltaCaptureC::smallBinsSmall Bins
- deltaCaptureC::smallSetOfSmallBinsSmall Bins
- deltaCaptureC::smallerDeltaSEA subset of miniDeltaSE.
- deltaCaptureC::viewpointRegionRegion surrounding the viewpoint
- deltaCaptureC::weightsExampleBinsWeights example bins
- deltaCaptureC::weightsExampleGrWeights example
- deltaGseg::pvalspvalues data
- deltaGseg::simtrajSample trajectory series
- deltaGseg::simtraj.trSample trajectory series
- deltaGseg::simtraj.tr2Sample trajectory series
- deltaGseg::traj1Sample trajectory series
- deltaGseg::traj1.denoiseSample trajectory series
- deltaGseg::traj1.ssSample trajectory series
- deltaGseg::traj1.trSample trajectory series
- DeMAND::bcellAnnoAnnotation for the expression data
- DeMAND::bcellExpB cell expression data
- DeMAND::bcellNetworkB cell network
- DeMAND::caseIndexCase sample index
- DeMAND::controlIndexControl sample index
- DeMixT::test.data.2compSimulated two-component test data
- DeMixT::test.data.3compSimulated three-component mixed cell line test data
- demuxmix::csfHashtag oligonucleotide (HTO) counts from 2,590 droplets
- demuxSNP::commonvariants_1kgenomes_subsetSample vcf file
- demuxSNP::multiplexed_scrnaseq_sceSingleCellExperiment object containing multiplexed RNA and HTO data from six biological smamples
- demuxSNP::vartrix_consensus_snpsSample VarTrix output
- DEP::DiUbiDiUbi - Ubiquitin interactors for different diubiquitin-linkages (UbIA-MS dataset)
- DEP::DiUbi_ExpDesignExperimental design of the DiUbi dataset
- DEP::UbiLengthUbiLength - Ubiquitin interactors of different linear ubiquitin lengths (UbIA-MS dataset)
- DEP::UbiLength_ExpDesignExperimental design of the UbiLength dataset
- DepecheR::testDataA 14 color flow cytometry dataset for example execution and playing around
- DepecheR::testDataDepecheA depeche clustering of the testData set
- DepecheR::testDataSNESNE of the testData set
- DepInfeR::drug_response_GDSCdrug_response_GDSC
- DepInfeR::mutation_GDSCmutation_GDSC
- DepInfeR::responseInputresponseInput
- DepInfeR::targetInputtargetInput
- DepInfeR::targetMatrixtargetMatrix
- DepInfeR::targetsGDSCtargetsGDSC
- derfinder::genomeDataGenome samples processed data
- derfinder::genomeDataRawGenome samples processed data
- derfinder::genomeFstatsF-statistics for the example data
- derfinder::genomeInfoGenome samples information
- derfinder::genomeRegionsCandidate DERs for example data
- derfinder::genomicStateGenomic State for Hsapiens.UCSC.hg19.knownGene
- DEsingle::countsTestData: A test dataset for DEsingle
- DEsingle::groupTestData: A test dataset for DEsingle
- DESpace::LIBD_subsetSubset from the human DLPFC 10x Genomics Visium dataset of the 'spatialLIBD' package
- DESpace::results_DESpace_testResults from 'DESpace_test' function
- DESpace::results_individual_testResults from 'individual_test' function
- destiny::guoGuo at al. mouse embryonic stem cell qPCR data
- destiny::guo_normGuo at al. mouse embryonic stem cell qPCR data
- DEWSeq::SLBP_K562_w50s20ENCODE eCLIP data for SLBP in K562, low count filtered
- DEWSeq::slbpDdsENCODE eCLIP data SLBP in K562
- DEWSeq::slbpRegionsENCODE eCLIP data SLBP in K562
- DEWSeq::slbpVstENCODE eCLIP data SLBP in K562
- DEWSeq::slbpWindowsENCODE eCLIP data SLBP in K562
- DFP::rmadatasetA sample ExpressionSet object
- DIAlignR::XIC_QFNNTDIVLLEDFQK_3_DIAlignRExtracted-ion chromatograms (XICs) of a peptide
- DIAlignR::alignObj_DIAlignRAlignment object of a peptide.
- DIAlignR::masterXICs_DIAlignRMaster fragment-ion chromatograms from two parents
- DIAlignR::multipeptide_DIAlignRAnalytes information from multipeptide.
- DIAlignR::oswFiles_DIAlignRAnalytes information from osw files
- DiffBind::tamoxifenTamoxifen resistance dataset used for DBA examples
- DiffBind::tamoxifenTamoxifen resistance dataset used for DBA examples
- DiffBind::tamoxifenTamoxifen resistance dataset used for DBA examples
- DiffBind::tamoxifen.greylistTamoxifen resistance dataset used for DBA examples
- diffcoexp::exprs.1exprs.1
- diffcoexp::exprs.2exprs.2
- diffGeneAnalysis::rawdataMicro array dataset
- diffuStats::graph_toyToy graph to play with diffusion
- diffUTR::example_bin_seExample bin-level 'RangedSummarizedExperiment'
- diffUTR::example_gene_annotationExample gene annotation
- diffUTR::rn6_PASPoly-A sites compendium for Rattus Norvegicus (Rno6)
- Dino::multimodalDatPlot data from simulated expression
- Dino::pbmcSmallSubset of 500 peripheral blood mononuclear cells (PBMCs) from a healthy donor
- Dino::unimodalDatPlot data from simulated expression
- dinoR::NomeDataNOMeseq data for WT and AdnpKO mouse ES cells
- Director::mesenchymalAnalysis results of Yang et al.'s (2013) master microRNA regulatory network
- Director::poorprogAnalysis results for poor prognosis serous ovarian cancer
- DirichletMultinomial::bestgrpData objects used for examples and the vignette
- DirichletMultinomial::fitData objects used for examples and the vignette
- DirichletMultinomial::xvalData objects used for examples and the vignette
- discordant::TCGA_Breast_RNASeqTCGA Breast Cancer RNASeq Sample Dataset
- discordant::TCGA_Breast_RNASeq_voomTCGA Breast Cancer RNASeq Sample Dataset
- discordant::TCGA_Breast_miRNASeqExample breast miRNA-Seq count dataset.
- discordant::TCGA_Breast_miRNASeq_voomExample breast miRNA-Seq voom-transformed count dataset.
- discordant::TCGA_GBM_miRNA_microarrayTCGA Glioblastoma Multiforme miRNA Sample Dataset
- discordant::TCGA_GBM_transcript_microarrayTCGA Glioblastoma Multiforme Transcript Sample Dataset
- DiscoRhythm::discoODAexclusionMatrixAlgorithm Exclusion Matrix
- DiscoRhythm::discoODAid2nameMapping Identifiers to Full Names
- distinct::Kang_subsetSubset from the 'Kang18_8vs8()' object of the 'muscData' package.
- distinct::resResults from 'distinct_test' function
- dittoSeq::demuxlet.exampledemuxlet.example
- divergence::breastTCGA_ERER positive or negative status of breast tumor samples
- divergence::breastTCGA_GroupNormal or Tumor status of breast samples
- divergence::breastTCGA_MatGene expression for 260 genes in 887 breast samples
- divergence::msigdb_HallmarksCancer Hallmark gene sets from the MSigDB collection
- dks::PSimulated null p-values from the uniform distribution.
- DMRcaller::DMRsNoiseFilterCGThe DMRs between WT and met1-3 in CG context
- DMRcaller::GEsThe genetic elements data
- DMRcaller::methylationDataListThe methylation data list
- DMRcaller::syntheticDataReplicatesSimulated data for biological replicates
- DMRScan::DMRScan.methylationDataDMRScan
- DMRScan::DMRScan.phenotypesDMRScan
- dmrseq::BS.chr21BS.chr21: Whole-genome bisulfite sequencing for chromosome 21 from Lister et al.
- dmrseq::annot.chr21annot.chr21: Annotation information for chromosome 21, hg38 genome
- dmrseq::dmrs.exdmrs.ex: Example results of DMRs
- DNAcopy::coriellArray CGH data set of Coriell cell lines
- DNAcopy::cytoBandCytogenic band data
- DNAcopy::default.DNAcopy.bdrySequential stopping boundary
- DominoEffect::DominoDataSample data
- DominoEffect::SnpDataSample data
- DominoEffect::TestDataSample data
- dominoSignal::CellPhoneDBCellPhoneDB subset
- dominoSignal::PBMCPBMC RNAseq data subset
- dominoSignal::SCENICSCENIC AUC subset
- Doscheda::doschedaDataPeptide Intensity data set for Doscheda
- Doscheda::processedExampleProcessed Peptide Intensity data set for Doscheda
- DOSE::DGN_EXTID2PATHIDDatasets
- DOSE::DGN_PATHID2EXTIDDatasets
- DOSE::DGN_PATHID2NAMEDatasets
- DOSE::NCG_EXTID2PATHIDDatasets
- DOSE::NCG_PATHID2EXTIDDatasets
- DOSE::NCG_PATHID2NAMEDatasets
- DOSE::VDGN_EXTID2PATHIDDatasets
- DOSE::VDGN_PATHID2EXTIDDatasets
- DOSE::VDGN_PATHID2NAMEDatasets
- DOSE::geneListDatasets
- doseR::hmel.datHmel data set
- doseR::seHmel data set
- doubletrouble::cds_scerevisiaeCoding sequences (CDS) of S. cerevisiae
- doubletrouble::diamond_interInterspecies DIAMOND output for yeast species
- doubletrouble::diamond_intraIntraspecies DIAMOND output for S. cerevisiae
- doubletrouble::fungi_kaksDuplicate pairs and Ka, Ks, and Ka/Ks values for fungi species
- doubletrouble::gmax_ksDuplicate pairs and Ks values for Glycine max
- doubletrouble::yeast_annotGenome annotation of the yeast species S. cerevisiae and C. glabrata
- doubletrouble::yeast_seqProtein sequences of the yeast species S. cerevisiae and C. glabrata
- drawProteins::five_rel_dataDataframe features of 5 human NFkappaB proteins Uniprot on 1 Nov 2017
- drawProteins::five_rel_listFeatures of five human Rel A proteins
- drawProteins::protein_jsonUniprot infor human Rel A protein in JSON format
- drawProteins::rel_A_featuresFeatures of human Rel A protein
- drawProteins::rel_jsonHuman Rel A protein features in JSON format
- drawProteins::tnfs_dataDataframe features of 2 human TNF receptors from Uniprot on 3 Jan 2018
- DriverNet::sampleDriversListSample DriverNet result
- DriverNet::sampleGeneNamesSample gene names
- DriverNet::sampleInfluenceGraphSample influence graph
- DriverNet::samplePatientExpressionMatrixSample patient expression matrix
- DriverNet::samplePatientMutationMatrixSample patient mutation matrix
- DriverNet::samplePatientOutlierMatrixSample patient outlier matrix
- DriverNet::sampleRandomDriversResultSample Result from computeRandomizedResult
- DrugVsDisease::customClustCustom Clusters
- DrugVsDisease::customDBCustom Gene Expression Profiles
- DrugVsDisease::customedgeEdge attributes for example custom network
- DrugVsDisease::customsifSIF file for custom clusters
- DrugVsDisease::profilesGene Expression Profiles
- DrugVsDisease::selprofileList: Differential gene expression and p-values
- DSS::RRBSAn example dataset for multiple factor design
- DSS::designExperimental design for the example RRBS dataset
- DSS::seqDataA simulated 'SeqCountData' object.
- dStruct::lai2019_Saccharomyces cerevisiae_ Structure-seq data
- dStruct::wan2014_Homo sapiens_ PARS data
- DTA::Dm.tnumberThe amount of thymines in the cDNA of each transcript of Drosophila Melanogaster.
- DTA::Hs.datamatGene expression profiles of the Homo Sapiens DTA experiment from Doelken et al.
- DTA::Hs.enst2ensgMapping of Homo Sapiens gene and transcript identifiers.
- DTA::Hs.phenomatDesign of the Homo Sapiens DTA experiment from Doelken et al.
- DTA::Hs.reliableGene identifiers valid for parameter estimation from the Homo Sapiens Doelken et al. DTA experiment.
- DTA::Hs.tnumberThe amount of thymines in the cDNA of each transcript of Homo Sapiens.
- DTA::Hs.tnumberThe amount of thymines in the cDNA of each transcript of Homo Sapiens.
- DTA::Mm.datamatGene expression profiles of the Mus Musculus DTA experiment from Doelken et al.
- DTA::Mm.enst2ensgMapping of Mus Musculus gene and transcript identifiers.
- DTA::Mm.phenomatDesign of the Mus Musculus DTA experiment from Doelken et al.
- DTA::Mm.reliableGene identifiers valid for parameter estimation from the Mus Musculus Doelken et al. DTA experiment.
- DTA::Mm.tnumberThe amount of thymines in the cDNA of each transcript of Mus Musculus.
- DTA::Mm.tnumberThe amount of thymines in the cDNA of each transcript of Mus Musculus.
- DTA::Pol.phenomatDesign of the Saccharomyces Cerevisiae rpb1-N488D (Slow Polymerase) cDTA experiment from Sun et al.
- DTA::Raw.datamatGene expression profiles of the Saccharomyces Cerevisiae rpb1-N488D (Slow Polymerase) and wild-type cDTA experiment from Sun et al.
- DTA::Sc.affy2ensgMapping of SaccharomycesCerevisiae Affymetrix Yeast 2.0 and gene identifiers.
- DTA::Sc.datamatGene expression profiles of the Saccharomyces Cerevisiae wild-type DTA experiment from Miller et al.
- DTA::Sc.datamat.dynamicGene expression profiles of the Saccharomyces Cerevisiae salt stress DTA experiment from Miller et al.
- DTA::Sc.ensg.reliableGene identifiers valid for parameter estimation from the Saccharomyces Cerevisiae Sun et al. cDTA experiment.
- DTA::Sc.phenomatDesign of the Saccharomyces Cerevisiae wild-type DTA experiment from Miller et al.
- DTA::Sc.phenomat.dynamicDesign of the Saccharomyces Cerevisiae salt stress DTA experiment from Miller et al.
- DTA::Sc.reliableGene identifiers valid for parameter estimation from the Saccharomyces Cerevisiae Miller et al. wild-type DTA experiment.
- DTA::Sc.reliable.dynamicGene identifiers valid for parameter estimation from the Saccharomyces Cerevisiae Miller et al. salt stress DTA experiment.
- DTA::Sc.ribig.ensgRibosome biogenesis genes.
- DTA::Sc.rpg.ensgRibosomal protein genes.
- DTA::Sc.stress.ensgISA stress module.
- DTA::Sc.tf.ensgTranscription factors.
- DTA::Sc.tnumberThe amount of thymines in the cDNA of each transcript of Saccharomyces Cerevisiae.
- DTA::Sc.tnumberThe amount of thymines in the cDNA of each transcript of Saccharomyces Cerevisiae.
- DTA::Sc.tnumberThe amount of thymines in the cDNA of each transcript of Saccharomyces Cerevisiae.
- DTA::Sc.tnumberThe amount of thymines in the cDNA of each transcript of Saccharomyces Cerevisiae.
- DTA::Sp.affy.reliableGene identifiers valid for cDTA normalization from the Saccharomyces Cerevisiae Sun et al. cDTA experiment.
- DTA::Sp.tnumberThe amount of thymines in the cDNA of each transcript of Schizosaccharomyces Pombe.
- DTA::Wt.phenomatDesign of the Saccharomyces Cerevisiae wild-type cDTA experiment from Sun et al.
- Dune::clusMatA clustering matrix used to demonstrate the ari-merging process.
- Dune::nucleiCluster labels for a subset of the allen Smart-Seq nuclei dataset
- dupRadar::dupRadar_examplesExample data containing precomputed matrices for two RNASeq experiments
- EasyCellType::cellmarker_tissueTissues in CellMarker database.
- EasyCellType::clustermole_tissueTissues in Clustermole database.
- EasyCellType::gene_pbmcDifferential expressed marker genes in 9 clusters.
- EasyCellType::panglao_tissueTissues in Panglao database.
- EasyCellType::pbmc_dataPeripheral Blood Mononuclear Cells (PBMC) data.
- easyRNASeq::RobinsonDelhomme2014Dataset included in the package
- EBarrays::gouldA dataset of class matrix
- EBcoexpress::fiftyGenesThe fiftyGenes expression matrix
- EBSEA::exonCountsSubset of Pasilla Dataset
- EBSeq::GeneMatThe simulated data for two condition gene DE analysis
- EBSeq::IsoListThe simulated data for two condition isoform DE analysis
- EBSeq::IsoMultiListThe simulated data for multiple condition isoform DE analysis
- EBSeq::MultiGeneMatThe simulated data for multiple condition gene DE analysis
- ecolitk::ecoli.m52.genomeEscherichia coli data
- ecolitk::ecoli.operonEscherichia coli data
- ecolitk::ecoligenome.operonKnown operon in E.coli - data.frame
- ecolitk::ecoligenomeBNUMEnvironment for 'bnum' identifiers
- ecolitk::ecoligenomeBNUM2ENZYMEEnvironment for 'bnum' identifiers
- ecolitk::ecoligenomeBNUM2GENBANKEnvironment for 'bnum' identifiers
- ecolitk::ecoligenomeBNUM2GENEPRODUCTEnvironment for 'bnum' identifiers
- ecolitk::ecoligenomeBNUM2MULTIFUNEnvironment
- ecolitk::ecoligenomeBNUM2STRANDEnvironment
- ecolitk::ecoligenomeBNUM2SYMBOLEnvironment for 'bnum' identifiers
- ecolitk::ecoligenomeCHRLOCEscherichia coli data
- ecolitk::ecoligenomeMULTIFUN2GOmultiFun classification
- ecolitk::ecoligenomeSTRANDEscherichia coli data
- ecolitk::ecoligenomeSYMBOLEscherichia coli data
- ecolitk::ecoligenomeSYMBOL2AFFYEscherichia coli data
- ecolitk::ecoligenomeSYMBOL2BNUMEnvironment for 'bnum' identifiers
- ecolitk::multiFunmultiFun classification
- EDASeq::yeastGCGC-content of _S. Cerevisiae_ genes
- EDASeq::yeastLengthLength of _S. Cerevisiae_ genes
- edge::endotoxinGene expression dataset from Calvano et al. (2005) Nature
- edge::gibsonGene expression dataset from Idaghdour et al. (2008)
- edge::kidneyGene expression dataset from Rodwell et al. (2004)
- EDIRquery::gene_chrGene chromosome location
- EGAD::GO.humanGO - human
- EGAD::GO.mouseGO - mouse
- EGAD::GO.vocGene ontology vocabulary
- EGAD::attr.humanHuman GENCODE annotations (v22)
- EGAD::attr.mouseMouse GENCODE annotations (M7)
- EGAD::biogridBIOGRID v3.4.126
- EGAD::example_annotationsExample of annotations
- EGAD::example_binary_networkExample of binary network
- EGAD::example_coexpressionExample of binary network
- EGAD::example_neighbor_votingExample of binary network
- EGAD::genesGenes from BIOGRID v3.4.126
- EGAD::orthoGene orthologs
- EGAD::phenoPhenocarta
- EGSEA::arraydataExample dataset for 'egsea.ma'
- eiR::example_compoundsExample Compounds
- EmpiricalBrownsMethod::allPvalsData used in tests and examples.
- EmpiricalBrownsMethod::datData used in tests and examples.
- EmpiricalBrownsMethod::pathwaysData used in tests and examples.
- EmpiricalBrownsMethod::randDataData used in tests and examples.
- EnMCB::anno_matrixIlluminaHumanMethylation450kanno
- EnMCB::demo_MCBinformationMCB information.
- EnMCB::demo_dataExpression matrix of demo dataset.
- EnMCB::demo_survival_dataSurvival data of demo dataset.
- enrichViewNet::demoGOSTThe result of a functional enrichment analysis done with 'gprofiler2' (<https://cran.r-project.org/web/packages/gprofiler2/vignettes/gprofiler2.html>).
- enrichViewNet::parentalNapaVsDMSODEGThe result of a differential expression analysis done between napabucasin treated and DMSO control parental MiaPaCa2 cells. The cells were treated for 2 hours with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.
- enrichViewNet::parentalNapaVsDMSOEnrichmentThe result of an enrichment analysis has been done using the significantly differentially expressed genes between napabucasin treated and DMSO control parental MiaPaCa2 cells. The cells were treated for 2 hour with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.
- enrichViewNet::rosaNapaVsDMSODEGThe result of a differential expression analysis done between napabucasin treated and DMSO control MiaPaCa2 cells stably expressing the Rosa26 control vector. The cells were treated for 2 hours with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.
- enrichViewNet::rosaNapaVsDMSOEnrichmentThe result of an enrichment analysis that has been done using the significantly differentially expressed genes between napabucasin treated and DMSO control MiaPaCa2 cells stably expressing the Rosa26 control vector. The cells were treated for 2 hour with 0.5 uM napabucasin. The protocol to generate the RNA-seq is described in Froeling F.E.M. et al 2019.
- EpiCompare::CnR_H3K27acExample CUT&Run peak file
- EpiCompare::CnR_H3K27ac_picardExample Picard duplication metrics file 2
- EpiCompare::CnT_H3K27acExample CUT&Tag peak file
- EpiCompare::CnT_H3K27ac_picardExample Picard duplication metrics file 1
- EpiCompare::encode_H3K27acExample ChIP-seq peak file
- EpiCompare::hg19_blacklistHuman genome hg19 blacklisted regions
- EpiCompare::hg38_blacklistHuman genome hg38 blacklisted regions
- EpiCompare::mm10_blacklistMouse genome mm10 blacklisted regions
- EpiCompare::mm9_blacklistMouse genome mm9 blacklisted regions
- EpiDISH::DummyBeta.mDummy beta value matrix
- EpiDISH::LiuDataSub.mWhole blood example beta value matrix
- EpiDISH::cent12CT.mWhole blood reference of 12 blood cell subtypes for EPIC array
- EpiDISH::cent12CT450k.mWhole blood reference of 12 blood cell subtypes for 450k array
- EpiDISH::centBloodSub.mWhole blood reference of 188 tsDHS-DMCs and 7 blood cell subtypes
- EpiDISH::centDHSbloodDMC.mWhole blood reference of 333 tsDHS-DMCs and 7 blood cell subtypes
- EpiDISH::centEpiFibFatIC.mReference for breast tissue
- EpiDISH::centEpiFibIC.mReference for genenric epithelial tissue
- epigenomix::eSetExample gene expression data set.
- epigenomix::fpkmExample RNA-seq data set.
- epigenomix::mappedReadsMapped reads obtained from a anti-histone ChIP-seq experiment.
- epigenomix::transToTSSA data frame with Ensemble transcript IDs and transcriptional start sites.
- epigraHMM::helas3ENCODE ChIP-seq broad data from Helas3 cell line
- epimutacions::GRsetGRset
- epimutacions::res.epi.manovares.epi.manova
- epiNEM::sameith_GOgraph-based GO similarity scores, string GO annotations for Sameith et al., 2015 data
- epiNEM::sameith_stringsig. of string interaction scores for Sameith et al., 2015 data
- epiNEM::samscreenExample data: epiNEM results for the Sameith et al., 2015 knock-out screen
- epiNEM::simExample data: simulation results
- epiNEM::wageningen_GOgraph-based GO similarity scores, string GO annotations for van Wageningen et al., 2015 data
- epiNEM::wageningen_stringsig. of string interaction scores for van Wageningen et al., 2010 data
- epiNEM::wagscreenExample data: epiNEM results for the Wageningen et al., 2010 knock-out screen "http://www.holstegelab.nl/publications/GSTF_geneticinteractions/ downloads/del_mutants_limma.txt"
- epiregulon.extra::regulonregulon created using 'epiregulon' package from reprogram-seq data
- epistack::stackepiepistack example and test dataset
- epistack::stackepi_grepistack backward compatibility dataset
- epistasisGA::caseGenotypes for the affected children of case-parent triads.
- epistasisGA::case.gxeGenotypes for the cases of case-parent triads with a simulated gene environment interaction.
- epistasisGA::case.mciGenotypes for the affected cases of case-parent triads with a simulated maternal-fetal interaction.
- epistasisGA::dadGenotypes for the fathers of case-parent triads.
- epistasisGA::dad.gxeGenotypes for the fathers of case-parent triads with a simulated gene environment interaction.
- epistasisGA::dad.mciGenotypes for the fathers of case-parent triads with a simulated maternal-fetal interaction.
- epistasisGA::exposureExposures for the cases of case-parent triads with a simulated gene environment interaction.
- epistasisGA::momGenotypes for the mothers of case-parent triads.
- epistasisGA::mom.gxeGenotypes for the mothers of case-parent triads with a simulated gene environment interaction.
- epistasisGA::mom.mciGenotypes for the mothers of case-parent triads with a simulated maternal-fetal interaction.
- epistasisGA::snp.annotationsRSID, REF, and ALT annotations for example dataset SNPs
- epistasisGA::snp.annotations.mciRSID, REF, and ALT annotations for example dataset SNPs
- EpiTxDb::rmbase_dataEpiTxDb internal data
- epivizr::tcga_colon_blocksExample methylation data (blocks) for epivizr vignette.
- epivizr::tcga_colon_curvesExample methylation data (smoothed methylation levels) for epivizr vignette
- epivizr::tcga_colon_expressionExample exon-level RNAseq data from TCGA project for epivizr vignette.
- epivizrChart::bcode_esetExample expression data from the Gene Expression barcode project
- epivizrChart::cgi_grLocations of CpG Islands
- epivizrChart::sumexpExample SummarizedExperiment for epivizr vignette
- epivizrChart::tcga_colon_blocksExample methylation data (blocks) for epivizr vignette.
- epivizrChart::tcga_colon_curvesExample methylation data (smoothed methylation levels) for epivizr vignette
- epivizrChart::tcga_colon_expressionExample exon-level RNAseq data from TCGA project for epivizr vignette.
- erccdashboard::ERCCDefERCCDef dataframe
- erccdashboard::ERCCMix1and2ERCCMix1and2 dataframe
- erccdashboard::MET.CTL.countDatRat toxicogenomics count data
- erccdashboard::MET.CTL.totalReadsRat toxicogenomics total read data
- erccdashboard::UHRR.HBRR.arrayDatUHRR and HBRR Illumina BeadArray data
- erccdashboard::UHRR.HBRR.countDatUHRR and HBRR RNA-Seq Illumina count data
- erccdashboard::UHRR.HBRR.totalReadsUHRR and HBRR sample total read data
- ERSSA::combinations.partialExample list of combinations generated by comb_gen function.
- ERSSA::condition_table.fullExample table of sample names and conditions
- ERSSA::condition_table.partialExample table of sample names and conditions
- ERSSA::count_table.filtered.partialExample count table of GTEx RNA-seq experiment, fitered by count_filter function
- ERSSA::count_table.fullExample count table of GTEx RNA-seq experiment
- ERSSA::count_table.partialExample count table of GTEx RNA-seq experiment
- ERSSA::deg.partialExample list of DE genes generated by edgeR
- escape::escape.gene.setsBuilt-In Gene Sets for escape
- eudysbiome::diffGeneraDifferential microbes in Genus-Species table A data frame containing 10 differential genera and the species included, which was to be annotated as '"harmful"' or '"harmless"'.
- eudysbiome::harmGeneraManually curated genera annotation table A data frame containing 260 genera annotated as "harmful" and the harmful species included in these genera.
- eudysbiome::microCountMicrobial count contingency table
- eudysbiome::microDiffDifferential annotated genera with abundance variations among pair-wise condition comparisons
- evaluomeR::bioMetricsDataset: Metrics for biological pathways
- evaluomeR::ontMetricsDataset: Structural ontology metrics
- evaluomeR::rnaMetricsDataset: RNA quality metrics
- EventPointer::AllEvents_RNASeqAlternative splicing events detected by EventPointer
- EventPointer::AllEvents_RNASeq_MPAlternative splicing multi-path events detected by EventPointer
- EventPointer::ArrayDatamultipathPreprocessed arrays data with multi-path events
- EventPointer::ArraysDataPreprocessed arrays data
- EventPointer::EventXtransrelationship between isoforms and events
- EventPointer::FitResult of EventPointer_Bootstrap
- EventPointer::MyPrimersData frame with primers design for conventional PCR
- EventPointer::MyPrimers_taqmanData frame with primers design for taqman PCR
- EventPointer::PSIssrelationship between isoforms and events
- EventPointer::SG_RNASeqSplicing graph elements predicted from BAM files
- EventPointer::SG_reclassifySplicing graph example for Events_ReClassification function
- EventPointer::TxDTranscript x Protein Domain matrix: small matrix for examples
- ExiMiR::GSE19183Affybatch object for the raw data from GEO series GSE19183
- ExiMiR::GSE20122Affybatch object for the raw data from GEO series GSE20122
- ExiMiR::galenvR annotation environment for GEO series GSE20122
- ExpressionAtlas::allExpsA SimpleList containing some dummy Expression Atlas datasets
- ExpressionAtlas::atlasResA DataFrame listing some Expression Atlas experiments
- ExpressionAtlas::rnaseqExpsA SimpleList containing a dummy RNA-seq Expression Atlas dataset
- extraChIPs::ex_genesDatasets for an example region
- extraChIPs::ex_hicDatasets for an example region
- extraChIPs::ex_promDatasets for an example region
- extraChIPs::ex_transDatasets for an example region
- extraChIPs::grch37.cytobandsCytogenetic bands
- extraChIPs::grch38.cytobandsCytogenetic bands
- extraChIPs::peaksDatasets for the Fixed-Width Vignette
- extraChIPs::seDatasets for the Fixed-Width Vignette
- factDesign::estrogenMicroarray Data from an Experiment on Breast Cancer Cells
- factR::chrom_matched_query_gtfChromosome matched version of "query_gtf"
- factR::domains.knownExample output of predictDomains()
- factR::domains.outExample output of predictDomains()
- factR::matched_query_gtfSeqlevels and gene_id matched query data
- factR::new_query_gtfQuery data containing CDS information
- factR::query_cdsCDS from 4 transcripts entries of the same gene
- factR::query_exonsGRangeList of exons from 4 transcripts entries from query_gtf
- factR::query_gtfImported GTF file containing 4 transcript entries of the same gene
- factR::ref_cdsCDS from 2 reference transcripts entries of the same gene
- factR::ref_exonsExons from 2 reference transcripts entries of the same gene
- factR::ref_gtfImported GTF file containing 2 reference transcript entries of the same gene
- famat::MPINetDataThe variables in the environment variable 'MPINetData' of the system
- famat::compl_data_resultOutput of 'compl_data' function
- famat::genesList of genes.
- famat::interactions_resultOutput of 'interactions' function
- famat::listkPathway enrichment analysis results for KEGG pathways.
- famat::listrPathway enrichment analysis results for Reactome pathways.
- famat::listwPathway enrichment analysis results for Wikipathways pathways.
- famat::metaList of metabolites.
- fastLiquidAssociation::testmatExample results from fastMLA requiring all significance methods
- fastseg::coriellArray CGH data set of Coriell cell lines
- fastseg::fastsegDataExample data set for fastseg
- fCI::fci.datadata frame of gene expression
- fCI::multi.dimensional.fci.datadata frame of gene expression
- fdrame::designExperimental design
- fdrame::exp.arrNormalized Expression Array
- FEAST::YAn example single cell count expression matrix (Yan)
- FEAST::trueclassAn example single cell dataset for the cell label information (Yan)
- fedup::geneDoubleExample list of a background set and two sets of test genes to use for enrichment analysis.
- fedup::geneMultiExample list of a background set and multiple sets of test genes to use for enrichment analysis.
- fedup::geneSingleExample list of a background set and single set of test genes to use for enrichment analysis.
- fedup::pathwaysGMTNamed list of human pathway annotations obtained from a GMT file.
- fedup::pathwaysTXTExample list of SAFE terms obtained from a TXT file.
- fedup::pathwaysXLSXExample list of SAFE terms obtained from a XLSX file.
- FELLA::FELLA.sampleFELLA.DATA sample data
- FELLA::input.sampleA randomly generated list of affected metabolites
- fenr::exmpl_allExample set of background genes.
- fenr::exmpl_selExample set of selected genes.
- fenr::goGO-terms data downloaded for the vignette.
- fenr::go_speciesGO species
- fenr::yeast_deDifferential expression results for yeast RNA-seq.
- fgga::CfDataA set of characterized protein coding genes from the Cannis familiaris organism annotated to a target GO subgraph considering both experimental and electronic evidence.
- FGNet::FEA_toolsFGNet data
- FGNet::GOEvidenceCodesFGNet data
- FGNet::groupTypesFGNet data
- FGNet::organismsFGNet data
- fgsea::exampleExpressionMatrixExample of expression values obtained for GSE14308.
- fgsea::examplePathwaysExample list of mouse Reactome pathways.
- fgsea::exampleRanksExample vector of gene-level statistics obtained for Th1 polarization.
- findIPs::miller05miller05 data
- FindIT2::ATAC_normCountATAC normCount of E50h-72h in Chr5
- FindIT2::RNADiff_LEC2_GRRNA diff result from LEC2_GR VS LEC2_DMSO
- FindIT2::RNA_normCountRNA normCount of E50h-72h in Chr5
- FindIT2::TF_target_databaseTF-target database
- FindIT2::test_featureSettest_featureSet
- FindIT2::test_geneSettest_geneSet
- FLAMES::scmixology_lib10scMixology short-read gene counts - sample 2
- FLAMES::scmixology_lib10_transcriptsscMixology long-read transcript counts - sample 2
- FLAMES::scmixology_lib90scMixology short-read gene counts - sample 1
- flowAI::BcellsflowSet of B cells.
- flowBeads::beads1Dako beads on day 1
- flowBeads::beads2Dako beads on day 2
- flowBeads::cytocalmefCytocal config file
- flowBeads::dakomefDako config file
- flowBin::aml.sampleMultitube AML sample as example data for flowBin
- flowcatchR::MesenteriumSubsetA sample 'Frames' object
- flowcatchR::candidate.plateletsA sample 'ParticleSet' object
- flowCHIC::Results_overlapsDataset with labels and sums of informative pixels within the overlap area of the FCS files included to the package
- flowCHIC::Results_overlaps_incolDataset with labels and sums of informative pixels within the overlap area of the second downloadable dataset
- flowCHIC::Results_overlaps_mixDataset with labels and sums of informative pixels within the overlap area of the first downloadable dataset
- flowCHIC::Results_xorDataset with labels and intensity values of the FCS files included to the package
- flowCHIC::Results_xor_incolDataset with labels and intensity values of the second downloadable dataset
- flowCHIC::Results_xor_mixDataset with labels and intensity values of the first downloadable dataset
- flowCHIC::abiotic_incolDataset with abiotic data
- flowClean::synPerturbedSynthetically Perturbed FCS.
- flowClust::rituximabThe Rituximab Dataset
- flowCore::GvHDExtract of a Graft versus Host Disease monitoring experiment (Rizzieri et al., 2007)
- flowCut::flowCutDataA list containing two GvHD flow frames from flowCore
- flowCyBar::Abiotic_data_sampleDataset with abiotic data and sample names
- flowCyBar::Cell_number_sampleDataset with relative measured cell numbers and sample names
- flowCyBar::Corr_data_sampleDataset with correlation data and sample names
- flowFP::fs1Example FCS flowSet
- flowFP::fs2Example FCS flowSet
- flowFP::plate96 well plate data.
- flowGraph::fg_data_fcafg_data_fca
- flowGraph::fg_data_pos2fg_data_pos2
- flowGraph::fg_data_pos30fg_data_pos30
- flowMeans::xxSample
- flowMerge::flowClust.resA flowClust model fitted to the rituximab data for 1:10 clusters.
- flowPeaks::barcodeThe barcode dataset
- flowPeaks::barcode.cidThe barcode dataset
- flowPeaks::concaveThe concave dataset
- flowPeaks::concave.cidThe concave dataset
- flowPlots::adultsNeonatesThe adultsNeonates example data set of "stacked" data.
- flowPlots::marginalDFAn example of marginalData
- flowPlots::markerMatrixAn example of the markers data.
- flowPlots::pfdDFAn example of pfdData
- flowPlots::pfdPartsListAn example of pfdPartsData
- flowPlots::profileDFAn example of profileData
- flowSpecs::fullPanelA fully stained spectral cytometry sample
- flowSpecs::specMatSpectral unmixing matrix
- flowSpecs::unmixCtrlsUnmixing controls
- flowStats::BackGatingSample backgating results
- flowStats::ITNSample flow cytometry data
- flowTime::dipdoubletGateA gate for the set of all diploid doublets
- flowTime::dipsingletGateA gate for the set of all diploid singlet yeast cells
- flowTime::hapdoubletGateA gate for the set of all haploid doublets
- flowTime::hapsingletGateA gate for the set of all haploid singlets
- flowTime::yeastGateA gate for the set of all yeast cells
- flowVS::HDSample flow cytometry data from healthy individuals
- fmcsR::fmcstestSD file stored in 'SDFset' object
- fobitools::fobiFOBI Table File - Jul 23, 2021
- fobitools::fobi_termsFOBI's 'ontology_index' object - Jul 23, 2021
- fobitools::foodsFOBI Foods Table File - Feb 02, 2021
- fobitools::idmapFOBI Identifier Map File - Jul 18, 2021
- FuseSOM::risom_datIMC Breast Cancer Data Data from A spatial atlas of breast cancer progression using MIBI-TOF and tissue transcriptomics
- gage::bodsCommon gene set data collections
- gage::carta.gsCommon gene set data collections
- gage::egSymbMapping between Entrez Gene IDs and official symbols
- gage::go.gsCommon gene set data collections
- gage::gse16873GSE16873: a breast cancer microarray dataset
- gage::kegg.gsCommon gene set data collections
- gage::kegg.gs.diseCommon gene set data collections
- gage::khierCommon gene set data collections
- gage::korgCommon gene set data collections
- GARS::GARS_Fitness_scoreRNA-seq dataset for testing GARS
- GARS::GARS_classesRNA-seq dataset for testing GARS
- GARS::GARS_data_normRNA-seq dataset for testing GARS
- GARS::GARS_fit_listRNA-seq dataset for testing GARS
- GARS::GARS_pop_listRNA-seq dataset for testing GARS
- GARS::GARS_populRNA-seq dataset for testing GARS
- GARS::GARS_res_GAA GarsSelectedFeatures object for testing GARS
- GateFinder::marker.namesLPSData
- GateFinder::prop.markersLPSData
- GateFinder::rawdataLPSData
- gcatest::sim_genoSimulated data from PSD model
- gcatest::sim_traitSimulated data from PSD model
- gCrisprTools::alnPrecalculated alignment statistics of a crispr screen
- gCrisprTools::annAnnotation file for a mouse Crispr library
- gCrisprTools::esExpressionSet of count data from a Crispr screen with strong selection
- gCrisprTools::essential.genesArtificial list of 'essential' genes in the example Crispr screen included for plotting purposes
- gCrisprTools::fitPrecalculated contrast fit from a Crispr screen
- gCrisprTools::resultsDFPrecalculated gene-level summary of a crispr screen
- gcrma::affinity.spline.coefsSpline coefficients for estimation of affinity from probe sequence
- GDCRNATools::DEGAllOutput of 'gdcDEAnalysis' for downstream analysis
- GDCRNATools::enrichOutputOutput of 'gdcEnrichAnalysis' for visualization
- GDCRNATools::lncTargetmiRNA-lncRNA interactions
- GDCRNATools::mirCountsmiRNA counts data of TCGA-CHOL
- GDCRNATools::pcTargetmiRNA-mRNA interactions
- GDCRNATools::rnaCountsRNAseq counts data of TCGA-CHOL
- gDR::small_combo_dataSmall data.table with raw combo data used for processing via gDR
- gDR::small_dataSmall data.table with raw data used for processing via gDR
- GeDi::macrophage_KEGG_exampleA sample input RData file
- GeDi::macrophage_Reactome_exampleA sample input RData file
- GeDi::macrophage_topGO_exampleA sample input RData file
- GeDi::macrophage_topGO_example_smallA small sample input RData file
- GeDi::ppi_macrophage_topGO_example_smallPPI
- GeDi::sample_genesetA sample input text file
- GeDi::sample_geneset_brokenA broken input text file
- GeDi::sample_geneset_emptyAn empty input text file
- GeDi::sample_geneset_smallA small sample input text file
- GeDi::scores_macrophage_topGO_example_smallSample scores
- gemini::InputInput object from Big Papi
- gemini::ModelModel object from Big Papi
- gemini::countsBig Papi counts matrix
- gemini::guide.annotationBig Papi guide annotations
- gemini::sample.replicate.annotationBig Papi sample and replicate annotations
- genArise::SimonDataset: Little fragment of a microarray from IFC UNAM
- genArise::WT.datasetMicroarray from the IFC
- GeneBreak::copynumber.data.chr18CGHcall Example copynumber data hg18 chr18
- GeneBreak::copynumber.data.chr20CGHcall Example copynumber data hg18 chr20
- GeneBreak::copynumber.data.chr21CGHcall Example copynumber data hg18 chr21
- GeneBreak::ens.gene.ann.hg18Gene Annotation hg18
- GeneBreak::ens.gene.ann.hg19Gene Annotation hg19
- GeneBreak::ens.gene.ann.hg38Gene Annotation hg38
- geneClassifiers::exampleMAS5Example MAS5.0 ExpressionSet
- GeneExpressionSignature::exampleSetsample data, a subset of the C-MAP
- genefilter::tdataA small test dataset of Affymetrix Expression data.
- genefu::annot.exposGene expression, annotations and clinical data from the International Genomics Consortium
- genefu::annot.nkisGene expression, annotations and clinical data from van de Vijver et al. 2002
- genefu::annot.vdxsGene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
- genefu::claudinLowDataclaudinLowData for use in the claudinLow classifier. Data generously provided by Aleix Prat.
- genefu::data.exposGene expression, annotations and clinical data from the International Genomics Consortium
- genefu::data.nkisGene expression, annotations and clinical data from van de Vijver et al. 2002
- genefu::data.vdxsGene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
- genefu::demo.exposGene expression, annotations and clinical data from the International Genomics Consortium
- genefu::demo.nkisGene expression, annotations and clinical data from van de Vijver et al. 2002
- genefu::demo.vdxsGene expression, annotations and clinical data from Wang et al. 2005 and Minn et al 2007
- genefu::mod1Gene modules published in Desmedt et al. 2008
- genefu::mod2Gene modules published in Wirapati et al. 2008
- genefu::modelOvcAngiogenicModel used to classify ovarian tumors into Angiogenic and NonAngiogenic subtypes.
- genefu::pam50PAM50 classifier for identification of breast cancer molecular subtypes (Parker et al 2009)
- genefu::pam50.robustPAM50 classifier for identification of breast cancer molecular subtypes (Parker et al 2009)
- genefu::pam50.scalePAM50 classifier for identification of breast cancer molecular subtypes (Parker et al 2009)
- genefu::scmgene.robustSubtype Clustering Model using only ESR1, ERBB2 and AURKA genes for identification of breast cancer molecular subtypes
- genefu::scmod1.robustSubtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Desmedt et al 2008)
- genefu::scmod2.robustSubtype Clustering Model using ESR1, ERBB2 and AURKA modules for identification of breast cancer molecular subtypes (Desmedt et al 2008)
- genefu::sig.endoPredictSignature used to compute the endoPredict signature as published by Filipits et al 2011
- genefu::sig.gene70Signature used to compute the 70 genes prognosis profile (GENE70) as published by van't Veer et al. 2002
- genefu::sig.gene76Signature used to compute the Relapse Score (GENE76) as published in Wang et al. 2005
- genefu::sig.geniusGene Expression progNostic Index Using Subtypes (GENIUS) as published by Haibe-Kains et al. 2010.
- genefu::sig.ggiGene expression Grade Index (GGI) as published in Sotiriou et al. 2006
- genefu::sig.oncotypedxSignature used to compute the OncotypeDX signature as published by Paik et al 2004
- genefu::sig.pik3cagsGene expression Grade Index (GGI) as published in Sotiriou et al. 2006
- genefu::sig.tamr13Tamoxifen Resistance signature composed of 13 gene clusters (TAMR13) as published by Loi et al. 2008.
- genefu::sigOvcAngiogenicsigOvcAngiogenic dataset
- genefu::sigOvcCrijnssigOvcCrijns dataset
- genefu::sigOvcSpentzossigOcvSpentzos dataset
- genefu::sigOvcTCGAsigOvcTCGA dataset
- genefu::sigOvcYoshiharasigOvcYoshihara dataset
- genefu::ssp2003SSP2003 classifier for identification of breast cancer molecular subtypes (Sorlie et al 2003)
- genefu::ssp2003.robustSSP2003 classifier for identification of breast cancer molecular subtypes (Sorlie et al 2003)
- genefu::ssp2003.scaleSSP2003 classifier for identification of breast cancer molecular subtypes (Sorlie et al 2003)
- genefu::ssp2006SSP2006 classifier for identification of breast cancer molecular subtypes (Hu et al 2006)
- genefu::ssp2006.robustSSP2006 classifier for identification of breast cancer molecular subtypes (Hu et al 2006)
- genefu::ssp2006.scaleSSP2006 classifier for identification of breast cancer molecular subtypes (Hu et al 2006)
- GeneGA::wSetCodon Adaptation Index (CAI) w tables
- GeneGeneInteR::data.SNPMultiple genes dataset
- GeneGeneInteR::gene.pairA case-control dataset with two genes
- GeneMeta::NevinsIntensity data for 46 Affymetrix slides with tissue samples of breast tumors
- GeneNetworkBuilder::ce.IDsMapC.elegns gene name to wormbase identifier map
- GeneNetworkBuilder::ce.interactionmaptranscript regulatory map of _Caenorhabditis elegans_
- GeneNetworkBuilder::ce.mapIDsmap file for converting from wormbase identifier to _Caenorhabditis elegans_ gene name
- GeneNetworkBuilder::ce.miRNA.mapmicro RNA of _Caenorhabditis elegans_
- GeneNetworkBuilder::example.dataexample datasets for documentation
- GeneNetworkBuilder::hs.IDsMapmap file for converting gene name or sequence name of _Homo sapiens_ to Entrez identifier
- GeneNetworkBuilder::hs.interactionmaptranscript regulation map of _Homo sapiens_
- GeneNetworkBuilder::hs.mapIDsmap file for converting from Entrez identifier to _Homo sapiens_ gene name
- GeneNetworkBuilder::hs.miRNA.mapmicro RNA of _Homo sapiens_
- GeneOverlap::gs.RNASeqGenome size based on RNA-seq data
- GeneOverlap::hESC.ChIPSeq.listChIP-seq gene lists
- GeneOverlap::hESC.RNASeq.listRNA-seq gene lists
- geneplast::gpdata.gsA pre-processed dataset for the geneplast package.
- geneplast::ppi.gsA pre-processed igraph object for the geneplast package.
- geneplotter::IMCAEntrezLinkA function to plot a graph colored by expression data
- geneplotter::expressionSet133aA small dataset for testing
- GeneRegionScan::exampleProbeLevelSetExample Dataset of class 'ProbeLevelSet'
- GeneRegionScan::genomicgenomic sequence of gene in ProbeLevelSet
- GeneRegionScan::mrnamRNA sequence of gene in ProbeLevelSet
- GENESIS::HapMap_ASW_MXL_KINGmatMatrix of Pairwise Kinship Coefficient Estimates for the combined HapMap ASW and MXL Sample found with the KING-robust estimator from the KING software.
- GENESIS::sample_annotation_1KGAnnotation for 1000 genomes Phase 3 samples
- geNetClassifier::geneSymbolsGene symbols associated to human Ensemble IDs.
- geNetClassifier::leukemiasClassifierSample leukemias classifier
- GeneticsPed::Falconer5.1Pedigree and data examples
- GeneticsPed::Mrode2.1Pedigree and data examples
- GeneticsPed::Mrode3.1Pedigree and data examples
- GeneTonic::enrichr_output_macrophageA sample output from Enrichr
- GeneTonic::fgseaResA sample output from fgsea
- GeneTonic::gostres_macrophageA sample output from g:Profiler
- GeneTonic::res_macrophage_IFNg_vs_naiveA sample 'DESeqResults' object
- GeneTonic::topgoDE_macrophage_IFNg_vs_naiveA sample 'res_enrich' object
- geneXtendeR::ratGene transfer format (GTF) file for rat (Rattus_norvegicus.Rnor_6.0.84)
- geneXtendeR::samplepeaksinputSample peaks list to be used as input to geneXtendeR
- genoCN::init.Para.CNAInitial parameters for the HMM
- genoCN::init.Para.CNVInitial parameters for the HMM of genoCNV
- genoCN::snpDataSimulated LRR and BAF data for 17,348 SNPs on chromosome 22.
- genoCN::snpInfoInformation of 17,348 SNPs on chromosome 22.
- genomation::cageExample CAGE data set.
- genomation::cpgiExample CpG island data set.
- genomation::genesExample RefSeq genes data set.
- genomation::promotersExample promoter data set.
- GenomAutomorphism::aaindex1List of 571 Amino Acid Physicochemical Indexes from AAindex Database
- GenomAutomorphism::aaindex2List of 94 Amino Acid Matrices from AAindex
- GenomAutomorphism::aaindex3Statistical protein contact potentials matrices from AAindex ver.9.2
- GenomAutomorphism::alnSimulated 'DNAStringSet' class object
- GenomAutomorphism::autby_coefAutomorphisms between DNA Primate BRCA1 Genes Grouped by Coefficients
- GenomAutomorphism::autmAutomorphisms between DNA Sequences from two COVID-19 genomes
- GenomAutomorphism::autm_3dAutomorphisms between DNA Sequences from two COVID-19 genomes
- GenomAutomorphism::autm_z125Automorphisms between DNA Sequences from two COVID-19 genomes
- GenomAutomorphism::brca1_alnMultiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes.
- GenomAutomorphism::brca1_aln2Multiple Sequence Alignment (MSA) of Primate BRCA1 DNA repair genes.
- GenomAutomorphism::brca1_autmAutomorphisms between DNA Sequences from Primate BRCA1 Genes
- GenomAutomorphism::brca1_autm2Automorphisms between DNA Sequences from Primate BRCA1 Genes
- GenomAutomorphism::cdm_z64Codon Distance Matrices for the Standard Genetic Code on Z4
- GenomAutomorphism::covid_alnPairwise Sequence Alignment (MSA) of COVID-19 genomes.
- GenomAutomorphism::covid_autmAutomorphisms between DNA Sequences from two COVID-19 genomes
- GenomAutomorphism::cyc_alnMultiple Sequence Alignment (MSA) of Primate Somatic Cytochrome C
- GenomAutomorphism::cyc_autmAutomorphisms between DNA Sequences from Primate Cytochrome C Genes
- GenomAutomorphism::dna_phycheSome Physicochemical Properties of DNA bases
- genomeIntervals::iGenome Intervals examples
- genomeIntervals::jGenome Intervals examples
- genomeIntervals::kGenome Intervals examples
- GenomicDistributions::TSS_hg19hg19 TSS locations
- GenomicDistributions::cellTypeMetadataTable the maps cell types to tissues and groups
- GenomicDistributions::chromSizes_hg19hg19 chromosome sizes
- GenomicDistributions::exampleOpenSignalMatrix_hg19A dataset containing a subset of open chromatin regions across all cell types defined by ENCODE for Homo Sapiens hg19
- GenomicDistributions::geneModels_hg19hg38 gene models
- GenomicDistributions::setB_100Example BED file read with rtracklayer::import
- GenomicDistributions::vistaEnhancersExample BED file read with rtracklayer::import
- genomicInstability::geneLengthAverage length of human and mouse known genes
- genomicInstability::geneLengthAverage length of human and mouse known genes
- genomicInstability::genePositionChromosomal coordinate of human and mouse known genes
- genomicInstability::genePositionChromosomal coordinate of human and mouse known genes
- GenomicInteractions::hg19.refseq.transcriptsHuman Refseq transcripts from chr 17-18
- GenomicInteractions::hic_example_dataExample HiC dataset
- GenomicInteractions::mm9_refseq_promotersMouse Refseq promoters from chr 14-15
- GenomicInteractions::thymus_enhPutative enhancers from mouse thymus data
- GenomicPlot::gf5_genomicToy data for examples and testing of the 'GenomicPlot' package
- GenomicPlot::gf5_metaToy data for examples and testing of the 'GenomicPlot' package
- GenomicSuperSignature::droplistMeSH terms to be excluded in drawWordcloud function
- GenomicSuperSignature::filterListRAVs that will output with quality-control messages
- GenomicSuperSignature::miniAllZSubset of allZ matrix constructed from 8 CRC training datasets
- GenomicSuperSignature::miniRAVmodelRAVmodel from 536 studies, annotated with MSigDB C2
- GenomicSuperSignature::miniTCGASubset of TCGA-COAD and TCGA-BRCA RNA sequencing datasets
- GenomicSuperSignature::res_hcutSubset of allZ matrix constructed from 8 CRC training datasets
- GenProSeq::example_PTENExample Data for Protein Sequences
- GenProSeq::example_luxAExample Data for Protein Sequences
- GenVisR::HCC1395_GermlineGermline Calls
- GenVisR::HCC1395_NNormal BAM
- GenVisR::HCC1395_TTumor BAM
- GenVisR::LucCNsegTruncated CN segments
- GenVisR::PIK3CASubset MAF file for PIK3CA gene
- GenVisR::SNPlociIdentity snps
- GenVisR::brcaMAFTruncated BRCA MAF file
- GenVisR::cytoGenoCytogenetic banding dataset
- GenVisR::hg19chrhg19 chromosome boundaries
- GeoDiff::NBthDEmod2A demo example output list returned by function fitNBthDE
- GeoDiff::NBthmDEmod2A demo example output list returned by function fitNBthmDE
- GeoDiff::NBthmDEmod2slopeA demo example output list returned by function fitNBthmDE
- GeoDiff::demoDataA demo dataset for GeoMx Cancer Transcriptome Atlas (CTA) panel
- GeoDiff::kidneyA demo dataset for GeoMx Human Whole Transcriptome Atlas (WTA) panel
- GeoTcgaData::GSE66705_sample2a matrix of gene expression data in GEO
- GeoTcgaData::geneExpressa data.frame of gene expression data
- GeoTcgaData::gene_cova data.frame of gene length and GC content
- GeoTcgaData::kegg_livera matrix of gene expression data in TCGA
- GeoTcgaData::modulea matrix of module name, gene symbols, and the number of gene symbols
- GeoTcgaData::profilea matrix of gene expression data in TCGA
- GeoTcgaData::ventriclea matrix of gene expression data in GEO
- gg4way::airwayFitairwayFit data
- GGPA::simulationSimulation dataa for graph-GPA
- GIGSEA::MSigDB.KEGG.PathwayMSigDB.KEGG.Pathway
- GIGSEA::MSigDB.TFMSigDB.TF
- GIGSEA::MSigDB.miRNAMSigDB.miRNA
- GIGSEA::TargetScan.miRNATargetScan.miRNA
- GIGSEA::heart.metaXcanheart.metaXcan
- gINTomics::mirna_hsamiRNA IDs. Dataset containing lastly definition of miRNAs (Names, Accessions, Sequences, Families and others) from different miRBase versions (From miRBase version 6 to version 22).
- gINTomics::mmultiassay_ovExample data for a standard workflow. This is an example dataset containing a MultiAssayExperiment of 20 ovarian cancer (OVC) patients extracted from the Cancer Genome Atlas (TCGA) database. The object contains all the available input data types: Gene expression data, miRNA expression data, gene methylation data, gene Copy Number Variations and miRNA Copy Number Variations.
- GLAD::P20Public CGH data of Veltman
- GLAD::P9Public CGH data of Veltman
- GLAD::array1Bladder cancer CGH data
- GLAD::array2Bladder cancer CGH data
- GLAD::array3Bladder cancer CGH data
- GLAD::cytobandCytogenetic banding
- GLAD::gm00143Public CGH data of Snijders
- GLAD::gm01524Public CGH data of Snijders
- GLAD::gm01535Public CGH data of Snijders
- GLAD::gm01750Public CGH data of Snijders
- GLAD::gm02948Public CGH data of Snijders
- GLAD::gm03134Public CGH data of Snijders
- GLAD::gm03563Public CGH data of Snijders
- GLAD::gm03576Public CGH data of Snijders
- GLAD::gm04435Public CGH data of Snijders
- GLAD::gm05296Public CGH data of Snijders
- GLAD::gm07081Public CGH data of Snijders
- GLAD::gm07408Public CGH data of Snijders
- GLAD::gm10315Public CGH data of Snijders
- GLAD::gm13031Public CGH data of Snijders
- GLAD::gm13330Public CGH data of Snijders
- glmSparseNet::string.network.700.cacheCache of protein-protein network, as it takes some time to retrieve and process this will facilitate the vignette building
- GlobalAncova::bindataSimulated binary data
- GlobalAncova::colon.normalGene expression data
- GlobalAncova::colon.phenoCovariate information for the colon data
- GlobalAncova::colon.tumourGene expression data
- GlobalAncova::pathwaysCancer related pathways
- GlobalAncova::phenodataCovariate information for the van t'Veer data
- GlobalAncova::vantVeerGene expression data
- globalSeq::toydataToydata
- GloScope::example_SCESingleCellExperiment containing example inputs to GloScope
- GloScope::example_SCE_smallSingleCellExperiment containing example inputs to GloScope
- gmoviz::bright_colours_opaquegmoviz colour sets
- gmoviz::bright_colours_transparentgmoviz colour sets
- gmoviz::nice_coloursgmoviz colour sets
- gmoviz::pastel_coloursgmoviz colour sets
- gmoviz::rich_coloursgmoviz colour sets
- GMRP::SNP358.dataData of 358 SNPs
- GMRP::SNP368annot.dataAnnotation data of 368SNPs
- GMRP::beta.dataBeta Data Of SNP Regressed on Causal Variables and Disease
- GMRP::cad.databoldGWAS Meta-analyzed Data of Coronary Artery Disease
- GMRP::lpd.data*GWAS* Meta-analyzed Data of Lipoprotein Cholesterols
- GOexpress::AlvMacSample data from a RNAseq experiment.
- GOexpress::AlvMac_GOgenesExample of custom mapping between gene ontology identifiers and gene features.
- GOexpress::AlvMac_allGOExample of custom gene ontology annotations.
- GOexpress::AlvMac_allgenesExample of custom gene feature annotations.
- GOexpress::AlvMac_resultsSample output from the 'GO_analyse()' function on an RNAseq experiment.
- GOexpress::AlvMac_results.pValSample output from the 'pValue_GO()' function on an RNAseq experiment.
- GOexpress::microarray2datasetTable mapping probeset identifier prefixes to datasets in the Ensembl BioMart.
- GOexpress::prefix2datasetTable mapping Ensembl gene identifier prefixes to BioMart datasets.
- GOpro::exrtcgaExpressions of human genes.
- goProfiles::CD4LLidsEntrez identifiers for CD4-TCells example
- goProfiles::clustKidneyMF2Ready 2 cluster equivalence distance matrix obtained from the analysis of the "Kidney Dataset" at level 2 of the MF ontology
- goProfiles::diseaseIdsEntrez identifiers for disease-related genes in the OMIM database
- goProfiles::dominantIdsEntrez identifiers for disease-related genes in the OMIM database
- goProfiles::dominantIdsEBIEntrez identifiers for disease-related genes in the OMIM database
- goProfiles::dominantIdsNCBIEntrez identifiers for disease-related genes in the OMIM database
- goProfiles::drosophilaIdsEntrez identifiers for genes related with an eye mutation in drosophila
- goProfiles::hugoIdsEntrez Identifiers obtained from the Human Genome Organization
- goProfiles::kidneyGeneListsGene-lists related to kidney transplantation rejection
- goProfiles::michaudIdsEntrez identifiers for genes related with an eye mutation in drosophila
- goProfiles::morbidmapIdsEntrez identifiers for disease-related genes in the OMIM database
- goProfiles::ostrinIdsEntrez identifiers for genes related with an eye mutation in drosophila
- goProfiles::recessiveIdsEntrez identifiers for disease-related genes in the OMIM database
- goProfiles::recessiveIdsEBIEntrez identifiers for disease-related genes in the OMIM database
- goProfiles::recessiveIdsNCBIEntrez identifiers for disease-related genes in the OMIM database
- goProfiles::singh01EntrezIDsProstate cancer-related genes
- goProfiles::singh05EntrezIDsProstate cancer-related genes
- goProfiles::welsh01EntrezIDsProstate cancer-related genes
- goProfiles::welsh05EntrezIDsProstate cancer-related genes
- GOSemSim::gotblInformation content of GO terms
- goseq::genesAndrogen stimulation of prostate cancer Cell lines.
- goSorensen::BP.4An example of an object of class "equivSDhtestList" resulting from a call to 'equivSorensenTest'
- goSorensen::allOncoGeneLists7 gene lists possibly related with cancer
- goSorensen::allTabsAn example of an object of class "allTableList" resulting from a call to 'buildEnrichTable'
- goSorensen::allTabsBP.4An example of an object of class "tableList" resulting from a call to 'buildEnrichTable'
- goSorensen::boot.cancerEquivSorensenAn example of object of class "AllEquivSDhtest" resulting from a call to 'allEquivTestSorensen'
- goSorensen::cancerEquivSorensenAn example of an object of class "AllEquivSDhtest" resulting from a call to 'allEquivTestSorensen'
- goSorensen::pbtGeneLists14 gene lists possibly related with kidney transplant rejection
- goSorensen::tab_atlas.sanger_BP3Cross-tabulation of enriched GO terms at level 3 of ontology BP in two gene lists
- goSorensen::waldman_atlas.BP.4An example of an object of class "equivSDhtest" resulting from a call to function 'equivSorensenTest'
- goSTAG::goSTAG_example_gene_listsgoSTAG Example Gene Lists
- goSTAG::goSTAG_go_genes_humangoSTAG GO Genes (Human)
- goSTAG::goSTAG_go_genes_mousegoSTAG GO Genes (Mouse)
- goSTAG::goSTAG_go_genes_ratgoSTAG GO Genes (Rat)
- goSTAG::rat_cancer_therapeutics_gene_listsRat Cancer Therapeutics Gene Lists
- GOstats::BdistsDistance matrices for the BCR/ABL and NEG subgroups.
- GOstats::NdistsDistance matrices for the BCR/ABL and NEG subgroups.
- GOTHiC::filteredA GenomicRangesList object used as an example in the GOTHiC package
- goTools::affylistList of probe ids from Affymetrix hgu133a chip and Operon Version 2 Human oligos
- goTools::operonlistList of probe ids from Affymetrix hgu133a chip and Operon Version 2 Human oligos
- GrafGen::HpyloriDataH. pylori data
- GrafGen::example_metadataMetadata for examples
- GrafGen::grafGen_example_resultsExample results
- GrafGen::grafGen_reference_dataframeReference data results for plots
- GrafGen::grafGen_reference_resultsReference data results
- granulator::bulkRNAseq_ABISPBMCs expression profiles (ABIS dataset)
- granulator::groundTruth_ABISPBMCS true cell type proprotions (ABIS dataset)
- granulator::sigMatrix_ABIS_S0Signature matrix for deconvolution of PBMCs in 17 cell types
- granulator::sigMatrix_ABIS_S1Signature matrix for deconvolution of PBMCs in 13 cell types
- granulator::sigMatrix_ABIS_S2Signature matrix for deconvolution of PBMCs in 11 cell types
- granulator::sigMatrix_ABIS_S3Signature matrix for deconvolution of PBMCs in 9 cell types
- graph::IMCAAttrsKEGG Integrin Mediated Cell Adhesion graph
- graph::IMCAGraphKEGG Integrin Mediated Cell Adhesion graph
- graph::MAPKsigA graph encoding parts of the MAPK signaling pathway
- graph::MAPKsigA graph encoding parts of the MAPK signaling pathway
- graph::apopGraphKEGG apoptosis pathway graph
- graph::biocReposA graph representing the Bioconductor package repository
- graph::esetsFemaleMultiGraph edgeSet data
- graph::esetsMaleMultiGraph edgeSet data
- graph::graphExamplesA List Of Example Graphs
- graph::pancrCaIniA graph encoding parts of the pancreatic cancer initiation pathway
- GraphAT::PhenoclustersYeast Gene-Knockout Fitness Data Cluster Memberships
- GraphAT::caustonYeast mRNA Expression Data
- GraphAT::ccCMCell-Cycle Cluster Matrix
- GraphAT::depthmatBPMatrices of depth of association for pairs of YEAST genes with respect to each of the BP,CC and MF ontologies of the GO database
- GraphAT::depthmatCCMatrices of depth of association for pairs of YEAST genes with respect to each of the BP,CC and MF ontologies of the GO database
- GraphAT::depthmatMFMatrices of depth of association for pairs of YEAST genes with respect to each of the BP,CC and MF ontologies of the GO database
- GraphAT::giaeverYeast Gene-Knockout Fitness Data
- GraphAT::mRNAclustersYeast mRNA Expression Data Cluster Memberships
- GraphAT::nNamesccCell-Cycle Cluster Matrix
- GRENITS::Athaliana_ODEGene expression time series generated with ODE model
- GRENITS::Athaliana_ODE_4NoiseRepsGene expression time series generated with ODE model with added noise
- GreyListChIP::ce10.blacklistA 'GRanges' object representing ENCODE signal artefact or "black list" regions.
- GreyListChIP::ce11.blacklistA 'GRanges' object representing ENCODE signal artefact or "black list" regions.
- GreyListChIP::dm3.blacklistA 'GRanges' object representing ENCODE signal artefact or "black list" regions.
- GreyListChIP::dm6.blacklistA 'GRanges' object representing ENCODE signal artefact or "black list" regions.
- GreyListChIP::grch37.blacklistA 'GRanges' object representing ENCODE signal artefact or "black list" regions.
- GreyListChIP::grch38.blacklistA 'GRanges' object representing ENCODE signal artefact or "black list" regions.
- GreyListChIP::greyListA sample 'GreyList' object for use in examples.
- GreyListChIP::hg19.blacklistA 'GRanges' object representing ENCODE signal artefact or "black list" regions.
- GreyListChIP::hg38.blacklistA 'GRanges' object representing ENCODE signal artefact or "black list" regions.
- GreyListChIP::mm10.blacklistA 'GRanges' object representing ENCODE signal artefact or "black list" regions.
- GreyListChIP::mm9.blacklistA 'GRanges' object representing ENCODE signal artefact or "black list" regions.
- GRmetrics::inputCaseASimulated dose-response assay data (Case A)
- GRmetrics::inputCaseCSimulated dose-response assay data (Case C)
- GSALightning::expressionBreast Cancer Data from The Cancer Genome Atlas (TCGA)
- GSALightning::sampleInfoSample Information for the Breast Cancer Data from The Cancer Genome Atlas (TCGA)
- GSALightning::targetGenesTarget Genes of Distal Regulatory Elements
- GSAR::p53DataSetp53 Dataset of the NCI-60 Cell Lines
- GSCA::Oct4ESC_TGOct4 activated (+) and repressed (-) target genes in embryonic stem cells
- GSCA::STAT1_TGSTAT1 activated (+) target genes defined from experimental ChIP-seq data and literature survey.
- GSCA::geneIDdataHomologene data
- GSEAmining::genesets_selSelected gene sets as test
- gsean::GO_dmeGene Ontology terms with gene ID for Drosophila melanogaster
- gsean::KEGG_hsaKEGG pathways with gene symbol for human
- GSReg::geneExrsGSReg
- GSReg::junc.RPM.Simulated
- GSReg::phenotypes
- GUIDEseq::peaks.grexample cleavage sites
- GUIDEseq::uniqueCleavageEventsexample unique cleavage sites
- Gviz::axTrackData sets
- Gviz::biomTrackData sets
- Gviz::biomTrack2Data sets
- Gviz::bmTrackData sets
- Gviz::bmtData sets
- Gviz::conservationData sets
- Gviz::cpgIslandsData sets
- Gviz::cpgIslandsData sets
- Gviz::ctrackData sets
- Gviz::cyp2b10Data sets
- Gviz::denseAnnTrackData sets
- Gviz::dtHorizData sets
- Gviz::ensGenesData sets
- Gviz::fromData sets
- Gviz::gcContentData sets
- Gviz::geneDetailsData sets
- Gviz::geneModelsData sets
- Gviz::idTrackData sets
- Gviz::ideoTrackData sets
- Gviz::idxTrackData sets
- Gviz::itrackData sets
- Gviz::knownGenesData sets
- Gviz::refGenesData sets
- Gviz::snpLocationsData sets
- Gviz::toData sets
- Gviz::twoGroupsData sets
- GWAS.BAYES::SNPsA. Thaliana Genotype matrix
- GWAS.BAYES::YA. Thaliana Simulated Phenotype matrix
- GWAS.BAYES::kinshipA. Thaliana Kinship matrix
- gwascat::ebicat_2020_04_30serialized gwaswloc instance from april 30 2020, sample of 50000 records
- gwascat::efo.obo.gconvert a typical OBO text file to a graphNEL instance (using Term elements)
- gwascat::g17SMSnpMatrix instance from chr17
- gwascat::gg17Ngenotype matrix from chr17 1000 genomes
- gwascat::gr6.0_hg38image of locon6 in GRanges, lifted over to hg38
- gwascat::gw6.rs_17character vector of rs numbers for SNP on chr17
- gwascat::gwastaggerGRanges with LD information on 9998 SNP
- gwascat::locon6location data for 10000 SNP
- gwascat::low17SnpMatrix instance from chr17
- gwascat::si.hs.37Seqinfo for GRCh37
- gwascat::si.hs.38Seqinfo for GRCh38
- GWASTools::HLA.hg18HLA region base positions
- GWASTools::HLA.hg19HLA region base positions
- GWASTools::HLA.hg38HLA region base positions
- GWASTools::centromeres.hg18Centromere base positions
- GWASTools::centromeres.hg19Centromere base positions
- GWASTools::centromeres.hg38Centromere base positions
- GWASTools::pcaSnpFilters.hg18Regions of SNP-PC correlation to filter for Principal Component Analysis
- GWASTools::pcaSnpFilters.hg19Regions of SNP-PC correlation to filter for Principal Component Analysis
- GWASTools::pcaSnpFilters.hg38Regions of SNP-PC correlation to filter for Principal Component Analysis
- GWASTools::pseudoautosomal.hg18Pseudoautosomal region base positions
- GWASTools::pseudoautosomal.hg19Pseudoautosomal region base positions
- GWASTools::pseudoautosomal.hg38Pseudoautosomal region base positions
- GWASTools::relationsMeanVarMean and Variance information for full-sibs, half-sibs, first-cousins
- GWENA::gtex_exprTranscriptomic muscle data from GTEx consorsium RNA-seq data
- GWENA::gtex_traitsTraits data linked to samples in transcriptomic data from GTEx
- GWENA::kuehne_exprTranscriptomic data from the Kuehne et al. publication
- GWENA::kuehne_traitsTraits data linked to samples in transcriptomic data from the Kuehne et al. publication
- h5vc::basesMutation spectrum analyses
- hapFabia::chr1ASW1000GExample genotype data in 'vcf' format
- hapFabia::hapResExample result of 'hapFabia'
- hapFabia::mergedIBDsegmentListExample IBD segment list as a result of 'hapFabia'
- hapFabia::resExample result of 'spfabia'
- hapFabia::simuExample simulation data for 'hapFabia'
- Harshlight::simblemish simulations from 100.000 random chips
- Harshlight::sim.intblemish simulations from 100.000 random chips
- HDTD::VEGFmouseVascular Endothelial Growth Factor Mouse Dataset
- hdxmsqc::BRD4dfThis is data to be included in my package
- hdxmsqc::BRD4df_fullThis is data to be included in my package
- heatmaps::hmData for man page examples
- heatmaps::hm2Data for man page examples
- heatmaps::matData for man page examples
- heatmaps::rle_listData for man page examples
- heatmaps::string_setData for man page examples
- heatmaps::tata_pwmData for man page examples
- heatmaps::windowsData for man page examples
- HELP::base.stacking.thermodynamicsBase-stacking thermodynamic parameters
- HEM::mubcpGene expression data for mouse B cell development
- HEM::pbrainGene expression data for primate brains
- hermes::expression_setExample 'ExpressionSet' Data
- hermes::hermes_dataExample 'HermesData' Data
- hermes::multi_assay_experimentExample 'MultiAssayExperiment' Data
- hermes::summarized_experimentExample 'SummarizedExperiment' Data
- HERON::heffron2021_wuhanSARS CoV-2 Wuhan Peptide Binding Array Data
- HGC::PollenEmbeddings of the Pollen datasets in the principal component space.
- hiAnnotator::genesSample RefSeq genes annotation
- hiAnnotator::sitesSample Retrovirus Integration Sites data
- hiAnnotator::sites.ctrlControls for Sample Retrovirus Integration Sites data
- HIBAG::HLA_Type_TableFour-digit HLA types of a study simulated from HapMap CEU
- HIBAG::HapMap_CEU_GenoSNP genotypes of a study simulated from HapMap CEU genotypic data
- HicAggR::Beaf32_Peaks.gnrD.melanogaster Beaf-32 ChIP-seq.
- HicAggR::HiC_Ctrl.cmx_lstIn situ Hi-C control.
- HicAggR::HiC_HS.cmx_lstIn situ Hi-C heat treated.
- HicAggR::TADs_Domains.gnrD.melanogaster TADs.
- HicAggR::TSS_Peaks.gnrD.melanogaster Transcription starting sites.
- HiCcompare::HMEC.chr10Hi-C data from HMEC cell line - chromosome 10 at 500kb resolution
- HiCcompare::HMEC.chr22Hi-C data from HMEC cell line - chromosome 22 at 500kb resolution
- HiCcompare::NHEK.chr10Hi-C data from NHEK cell line - chromosome 10 at 500kb resolution
- HiCcompare::NHEK.chr22Hi-C data from NHEK cell line - chromosome 22 at 500kb resolution
- HiCcompare::brain_tableHi-C data from two regions of the brain at 100KB resolution
- HiCcompare::centromere_locationsLocations of the centromeres for hg19
- HiCcompare::coolerHi-C data in the cooler format
- HiCcompare::hg19_blacklistBED file for hg19 blacklisted regions
- HiCcompare::hg38_blacklistBED file for hg38 blacklisted regions
- HiCcompare::hmec.ISHi-C data from HMEC cell line - chromosome 22 at 500kb resolution
- HiCcompare::nhek.ISHi-C data from NHEK cell line - chromosome 22 at 500kb resolution
- HiCDOC::exampleHiCDOCDataSetExample HiCDOCDataSet.
- HiCDOC::exampleHiCDOCDataSetProcessedExample HiCDOCDataSet, filtered, normalized and with compartements detected.
- HiCExperiment::centros_yeastExample datasets provided in 'HiCExperiment' & 'HiContactsData'
- hierGWAS::simGWASSimulated GWAS data
- hierinf::simGWASSimulated GWAS data set
- hipathia::DAdataWilcoxon and limma comparison object for nodes, pathways and functional annotations
- hipathia::brcaBRCA gene expression dataset as SummarizedExperiment
- hipathia::brca_dataBRCA gene expression dataset
- hipathia::brca_designBRCA experimental design
- hipathia::compWilcoxon comparison of pathways object
- hipathia::exp_dataNormalized BRCA gene expression dataset
- hipathia::go_valsGene Ontology matrix of the BRCA gene expression dataset
- hipathia::hidataResults object
- hipathia::path_valsPathways matrix of the BRCA gene expression dataset
- hipathia::pathwaysPathways object including pathways has03320 and hsa04012.
- hipathia::resultsResults object
- HIPPO::ensg_hgncA reference data frame that matches ENSG IDs to HGNC symbols
- HIPPO::toydataA sample single cell sequencing data subsetted from Zheng2017
- hiReadsProcessor::pslPSL file output
- hiReadsProcessor::seqPropsSample Integration Sites Sequencing Data
- HiTC::E14HiTC - 5C data
- HiTC::MEFHiTC - 5C data
- hmdbQuery::hmdb1hmdb1: demonstration HMDB entry
- hmdbQuery::hmdb_diseasehmdb_disease: Sept 2017 extract from hmdb.ca of direct disease associations
- hmdbQuery::hmdb_genehmdb_gene: Sept 2017 extract from hmdb.ca of direct gene associations
- hmdbQuery::hmdb_omimhmdb_omim: Sept 2017 extract from hmdb.ca of direct omim associations
- hmdbQuery::hmdb_proteinhmdb_protein: Sept 2017 extract from hmdb.ca of direct protein associations
- HMMcopy::normal_copyHMMcopy example dataset
- HMMcopy::tumour_copyHMMcopy example dataset
- HMMcopy::tumour_paramHMMcopy example dataset
- HMMcopy::tumour_readsHMMcopy example dataset
- HMMcopy::tumour_segmentsHMMcopy example dataset
- hoodscanR::speExample test spatial transcriptomics data
- hopach::golubGene expression dataset from Golub et al. (1999)
- hopach::golub.clGene expression dataset from Golub et al. (1999)
- hopach::golub.gnamesGene expression dataset from Golub et al. (1999)
- HPAanalyze::hpa_histology_dataHPA histology dataset
- HPiP::Gold_ReferenceSetGold-standard Reference Set of Inter-Species PPIs
- HPiP::UP000464024_dfData.frame Containing SARS-CoV-2 FASTA Sequences
- HPiP::enrich.dfEnrichment Result
- HPiP::example_dataInput Data for Prediction Algorithm
- HPiP::host_seHost SummarizedExperiment object
- HPiP::predicted_PPIsPredicted HP-PPIs
- HPiP::unlabel_dataHP-PPIs with Unknown Class Labels
- HPiP::viral_seViral SummarizedExperiment object
- HTSFilter::sultanRNA-seq data from humans in Sultan et al. (2008)
- hummingbird::abnormMSample matrix
- hummingbird::abnormUMSample matrix
- hummingbird::exampleSECaseSample input data
- hummingbird::exampleSEControlSample input data
- hummingbird::normMSample matrix
- hummingbird::normUMSample matrix
- hummingbird::posSample matrix
- HybridExpress::deg_countsData frame with frequencies (absolute and relative) of DEGs per contrast
- HybridExpress::deg_listList of differentially expressed genes for all contrasts
- HybridExpress::go_chlamyData frame with GO terms annotated to each gene of Chlamydomonas reinhardtii
- HybridExpress::se_chlamyExpression data (in counts) for 3 Chlamydomonas lines (P1, P2, and F1)
- HybridMTest::GroupComp.dataSample ExpressionSet of GroupComp.data
- HybridMTest::correlation.dataSample ExpressionSet object of correlation.data
- iASeq::sampleASE_exprsExample Dataset for iASeq
- iASeq::sampleASE_refidExample Dataset for iASeq
- iASeq::sampleASE_repidExample Dataset for iASeq
- iASeq::sampleASE_studyidExample Dataset for iASeq
- iBMQ::PPA.liverA matrix with Posterior Probabilities of Association
- iBMQ::geneGene expression from whole eye tissue from n = 68 BXD RIS mice.
- iBMQ::geneposGene position data frame
- iBMQ::genotype.liverA set of 290 SNPs from 60 F2 mice.
- iBMQ::map.liverSNP position data frame
- iBMQ::phenotype.liverGene expression from liver tissue from n = 60 F2 mice.
- iBMQ::probe.liverGene position data frame
- iBMQ::snpA set of 1700 SNP from 68 BXD RIS mice.
- iBMQ::snpposSNP position data frame
- iCARE::bc_72_snpsData for examples
- iCARE::bc_incData for examples
- iCARE::bc_model_cov_infoData for examples
- iCARE::bc_model_formulaData for examples
- iCARE::bc_model_log_orData for examples
- iCARE::bc_model_log_or_post_50Data for examples
- iCARE::mort_incData for examples
- iCARE::new_cov_profData for examples
- iCARE::new_snp_profData for examples
- iCARE::outputData for examples
- iCARE::ref_cov_datData for examples
- iCARE::ref_cov_dat_post_50Data for examples
- iCARE::validation.cohort.dataData for examples
- iCARE::validation.nested.case.control.dataData for examples
- Icens::cmvData on times to shedding of cytomegalovirus and to colonization of mycobacterium avium complex.
- Icens::cosmesisThe time taken until cosmetic deterioration of breast cosmesis.
- Icens::hivIntervals for infection time and disease onset for 257 hemophiliac patients.
- Icens::pruittA small artificial, bivariate right-censored data set.
- iChip::oct4Oct4 data
- iChip::p53p53 data
- iClusterPlus::breast.chr17Breast cancer data set DNA copy number and mRNA expression measure on chromosome 17
- iClusterPlus::coordgenomic coordinates
- iClusterPlus::gbm.expGBM data
- iClusterPlus::gbm.mutGBM data
- iClusterPlus::gbm.segGBM data
- iClusterPlus::glpgood lattice points using the uniform design
- iClusterPlus::simuResultThe results for the analysis of the simulated data.
- iClusterPlus::variation.hg18.v10.nov.2010Human genome variants of the NCBI 36 (hg18) assembly
- iCNV::filenmName of the file
- iCNV::icnv_res0Example iCNV calling results.
- iCNV::ngs_bafBAF list from NGS
- iCNV::ngs_baf.chrBAF chromosome from NGS
- iCNV::ngs_baf.idBAF variants id from NGS
- iCNV::ngs_baf.nmBAF variants sample name from NGS
- iCNV::ngs_baf.posBAF position list from NGS
- iCNV::ngs_plrNormalized Poisson likelihood ratio list from NGS
- iCNV::ngs_plr.posExon location list from NGS
- iCNV::normObjDemo data pre-stored for normObj.
- iCNV::qcObjDemo data pre-stored for qcObj.
- iCNV::sampnameCODEX sample name
- iCNV::sampname_qcQCed sample name
- iCNV::snp_bafBAF list from Array
- iCNV::snp_baf.posBAF position list from Array
- iCNV::snp_lrrNormalized log R ratio list from Array
- iCNV::snp_lrr.posSNP position list from Array
- iCOBRA::cobradata_exampleExample data set with three differential gene expression methods
- iCOBRA::cobradata_example_svalExample data set with three differential gene expression methods
- IdeoViz::GSM733664_broadPeaksData for vignette example 4.
- IdeoViz::binned_fullGenomeData for example 3.
- IdeoViz::binned_multiSeriesData for vignette example 1.
- IdeoViz::binned_singleSeriesData for example 2.
- IdeoViz::hg18_ideoIdeogram table for hg18
- IdeoViz::winsData for vignette example 1.
- IdeoViz::winsData for vignette example 1.
- IdeoViz::wins_discreteData for example 2.
- IdeoViz::wins_discreteData for example 2.
- IdeoViz::wins_entiregenomeData for example 3.
- IdeoViz::wins_entiregenomeData for example 3.
- idiogram::Cf.cytobandCytogenetic Banding information
- idiogram::Hs.cytobandCytogenetic Banding information
- idiogram::Mm.cytobandCytogenetic Banding information
- idiogram::Rn.cytobandCytogenetic Banding information
- idiogram::colo.esetdata included for idiogram package examples
- idiogram::ucsf.chrdata included for idiogram package examples
- idiogram::vai.chrdata included for idiogram package examples
- idpr::DUNMatA Substitution Matrix for Aligning Intrinsically Disordered Proteins
- idpr::Disorder40Disorder-based Substitution Matrices.
- idpr::Disorder60Disorder-based Substitution Matrices.
- idpr::Disorder85Disorder-based Substitution Matrices.
- idpr::EDSSMat50EDSSMat Disorder-based Substitution Matrices.
- idpr::EDSSMat60EDSSMat Disorder-based Substitution Matrices.
- idpr::EDSSMat62EDSSMat Disorder-based Substitution Matrices.
- idpr::EDSSMat70EDSSMat Disorder-based Substitution Matrices.
- idpr::EDSSMat75EDSSMat Disorder-based Substitution Matrices.
- idpr::EDSSMat80EDSSMat Disorder-based Substitution Matrices.
- idpr::EDSSMat90EDSSMat Disorder-based Substitution Matrices.
- idpr::GorillaTP53Human Cellular tumor antigen p53 and homologs
- idpr::KDNormKyte and Doolittle Scaled Hydropathy Index
- idpr::TP53SequencesHuman Cellular tumor antigen p53 and homologs
- idpr::pKaDataSets of pKa values for Charged Amino Acids
- idr2d::chiapetExample Genomic Interaction Data Set
- idr2d::chipseqExample Genomic Peak Data Set
- idr2d::hicExample Hi-C data set
- iGC::hg19DBNMhg19-RefSeq
- IgGeneUsage::CDR3_EpitopesNet charge usage in CDR3 sequences of T-cell receptor repertoires disturbed by Influenza-A and CMV
- IgGeneUsage::IGHV_HCVIGHV gene usage in HCV+ and healthy individuals
- IgGeneUsage::IgIGHV gene family usage in vaccine-challenged B-cell repertoires
- IgGeneUsage::Ig_SEIGHV gene family usage in vaccine-challenged B-cell repertoires (SummarizedExperiment object)
- IgGeneUsage::d_zibb_1Simulated Ig gene usage data
- IgGeneUsage::d_zibb_2Simulated Ig gene usage data
- IgGeneUsage::d_zibb_3Simulated Ig gene usage data
- IgGeneUsage::d_zibb_4Simulated Ig gene usage data
- IgGeneUsage::d_zibb_5Simulated Ig gene usage data
- IgGeneUsage::d_zibb_6Simulated Ig gene usage data
- ILoReg::pbmc3k_500A toy dataset with 500 cells downsampled from the pbmc3k dataset.
- IMAS::Clinical.dataA data frame for clinical data
- IMAS::GroupSamGroup of each sample.
- IMAS::sampleMedataMethylation level data
- IMAS::sampleMelocusGenomic locus of methylations
- IMAS::samplebamfilesA data frame for example expression bam files.
- IMAS::samplesnpGenotype data
- IMAS::samplesnplocusGenomic locus of SNPs
- IMMAN::CeleganceCelegance
- IMMAN::FruitFlyFruit Fly
- IMMAN::H.sapiensHomo sapiens (Human)
- IMMAN::R.norvegicusRattus norvegicus (Rat)
- immunoClust::dat.expimmunoClust Meta-clustering Sample
- immunoClust::dat.fcsimmunoClust Cell-clustering Sample
- immunoClust::dat.metaimmunoClust Meta-clustering Results Sample
- impute::khanmissKhan microarray data with random missing values
- INDEED::Met_GUGU cirrhosis (CIRR) and GU Hepatocellular carcinoma (HCC) data.
- INDEED::Met_Group_GUGroup label.
- INDEED::Met_name_GUKEGG ID
- INDEED::pvalue_M_GUP-values obtained by differential expression (DE) analysis.
- iNETgrate::toyCleanedAmlA subset of cleaned TCGA-LAML data
- iNETgrate::toyComputElociA subset of weighted DNA methylation profile of TCGA-LAML data
- iNETgrate::toyEigengenesA subset of weighted average of gene expression present in each module
- iNETgrate::toyRawAmlA subset of TCGA-LAML data
- infercnv::HMM_statesinfercnv object result of the processing of run() in the HMM example, to be used for other examples.
- infercnv::infercnv_annots_exampleGenerated classification for 10 normal cells and 10 tumor cells.
- infercnv::infercnv_data_exampleGenerated SmartSeq2 expression data with 10 normal cells and 10 tumor cells. This is only to demonstrate how to use methods, not actual data to be used in an analysis.
- infercnv::infercnv_genes_exampleDownsampled gene coordinates file from GrCh37
- infercnv::infercnv_object_exampleinfercnv object result of the processing of run() in the example, to be used for other examples.
- infercnv::mcmc_objinfercnv object result of the processing of inferCNVBayesNet in the example, to be used for other examples.
- infinityFlow::steady_state_lungSubset of a massively parallel cytometry experiment of mouse lung single cells
- infinityFlow::steady_state_lung_annotationTarget and isotypes annotation for the data object infinityFlow::steady_state_lnug
- infinityFlow::steady_state_lung_backbone_specificationBackbone and Infinity antibodies specification for the data object infinityFlow::steady_state_lnug
- InPAS::utr3.mm10Annotation of 3' UTRs for mouse (mm10)
- INSPEcT::allcountsA list containing mature and nascent counts for exons and introns, three replicates and 11 time points: 0,1/6,1/3,1/2,1,1.5,2,4,8,12,16 hours.
- INSPEcT::featureWidthsContains two variables: "exWdths" and "intWdths" containing the lenght of the exons and introns, respectively, relative to the genes in "allcounts"
- INSPEcT::libsizesContains two variables: "nascentLS" and "totalLS" containing the sequencing depth of nascent and total libraries respectively, relative to the experiments in "allcounts"
- INTACT::exprwt_sumstatsTWAS weights for a simulated gene.
- INTACT::gene_set_listSimulated gene set list.
- INTACT::ld_sumstatsLD correlation matrix from a simulated data set.
- INTACT::multi_simdatSimulated TWAS, PWAS, and pairwise colocalization summary data.
- INTACT::protwt_sumstatsPWAS weights for a simulated gene.
- INTACT::simdatSimulated TWAS and colocalization summary data.
- INTACT::z_sumstatsTWAS and PWAS z-score for a simulated gene.
- InTAD::enhSelEnhancer signals subset detected from medulloblatoma samples
- InTAD::enhSelGRGenomic coordiantes of enhancer signals subet
- InTAD::loopsDfSelData frame containing coordinates of loops
- InTAD::mbAnnDataData frame containing information about samples
- InTAD::rpkmCountsSelGene expression subset from medulloblastoma samples
- InTAD::tadGRGenomic coordiantes of topologically associated domains
- InTAD::txsSelGenomic coordiantes of genes subset
- interacCircos::arcExampleArc plot example data
- interacCircos::bubbleExampleBubble plot example data
- interacCircos::chord.pExampleExample data of chord plot of circosJS
- interacCircos::chordExampleExample data of chord plot of NG-Circos
- interacCircos::cnvExampleCnv module example data
- interacCircos::geneExampleGene plot example data
- interacCircos::heatmapExampleHeatmap plot example data
- interacCircos::hg19_ideogramIdeogram for hg19
- interacCircos::histogramExampleHistogram plot example data
- interacCircos::lineExampleLine plot example data
- interacCircos::linkExampleLink plot example data
- interacCircos::lollipopExampleLollipop plot example data
- interacCircos::scatterExampleScatter plot example data
- interacCircos::snpExampleSnp plot example data
- interacCircos::wigExampleWig plot example data
- InteractiveComplexHeatmap::rand_matA random matrix
- interactiveDisplay::exprAn Example ExpressionSet object
- interactiveDisplay::mmgrAn Example GRanges Object
- interactiveDisplay::mmgrlAn Example GRangesList Object
- interactiveDisplay::seAn Example RangedSummarizedExperiment Object
- InterCellar::input.dataInput Data example
- IntEREst::mdsChr22ExObjObject of SummarizedExperiment type for exon-exon junction of MDS data
- IntEREst::mdsChr22IntSpObjObject of SummarizedExperiment type for intron spanning reads of MDS data
- IntEREst::mdsChr22ObjObject of SummarizedExperiment type for intron retention MDS data
- IntEREst::pwmU12dbPWM of U12 and U2-type introns splice sites
- IntEREst::u12U12 data
- IntramiRExploreR::Affy1_Distance_FinalTargets for the microRNA analyzed from Affy1 plaform using Distance.
- IntramiRExploreR::Affy1_Pearson_FinalTargets for the microRNA analyzed from Affy1 plaform using Pearson.
- IntramiRExploreR::Affy2_Distance_FinalTargets for the microRNA analyzed from Affy2 plaform using Distance.
- IntramiRExploreR::Affy2_Pearson_FinalTargets for the microRNA analyzed from Affy2 plaform using Pearson.
- IntramiRExploreR::miRNA_ID_to_FunctionContains the miRNA function information from Flybase database.
- IntramiRExploreR::miRNA_summary_DBContains the summary for the intragenic miRNA.
- iPAC::KRAS.MutationsKRAS.Mutations
- iPAC::PIK3CA.MutationsPIK3CA.Mutations
- iPath::GSDB_exampleexample gene set database (GSDB)
- iPath::prad_clisimulated clinical data for PRAD cancer patients
- iPath::prad_exprsexpression matrix for PRAD cancer patients in TCGA
- iPath::prad_indsnormal (0) and tumor (1) classes associated with PRAD expression data
- ISAnalytics::association_fileExample of association file.
- ISAnalytics::integration_matricesExample of imported multi-quantification integration matrices.
- ISAnalytics::proto_oncogenesData frames for proto-oncogenes (human and mouse) amd tumor-suppressor genes from UniProt.
- ISAnalytics::refGenes_hg19Gene annotation files for hg19, mm9 and mm10.
- ISAnalytics::refGenes_mm9Gene annotation files for hg19, mm9 and mm10.
- ISAnalytics::tumor_suppressorsData frames for proto-oncogenes (human and mouse) amd tumor-suppressor genes from UniProt.
- iSeq::nrsfnrsf data
- ISLET::GE600_seISLET deconvolution example raw input data
- ISLET::GE600age_seISLET example datasets for slope variable testing in csDE
- isobar::ib_phosphoIsobar Data packages
- isobar::ibspiked_set1Isobar Data packages
- isobar::ibspiked_set2Isobar Data packages
- isobar::noise.model.hcdIsobar Data packages
- IsoCorrectoR::IsoCorrectoRIsoCorrectoR example data
- IsoformSwitchAnalyzeR::exampleSwitchListExample data for IsoformSwitchAnalyzeR
- IsoformSwitchAnalyzeR::exampleSwitchListAnalyzedExample data for IsoformSwitchAnalyzeR
- IsoformSwitchAnalyzeR::exampleSwitchListIntermediaryExample data for IsoformSwitchAnalyzeR
- ISoLDE::filteredASRcountsNORMALIZED AND FILTERED ALLELE SPECIFIC READ (ASR) COUNTS FOR AN EXPERIENCE WITH MORE THAN TWO REPLICATES
- ISoLDE::normASRcountsNORMALIZED ALLELE SPECIFIC READ (ASR) COUNTS FOR AN EXPERIENCE WITH MORE THAN TWO REPLICATES
- ISoLDE::rawASRcountsRAW ALLELE SPECIFIC READ (ASR) COUNTS FOR AN EXPERIENCE WITH MORE THAN TWO REPLICATES
- ISoLDE::targetMETADATA ABOUT THE ASR COUNT DATA.
- isomiRs::dat286.longData frame containing mirna from Argyropoulos's paper
- isomiRs::egoenrichResult class
- isomiRs::gene_ex_rseData frame containing gene expression data
- isomiRs::ma_exData frame containing gene-mirna relationship
- isomiRs::mirDataExample of IsomirDataSeq with human brain miRNA counts data
- isomiRs::mirTritationData frame containing mirna from Argyropoulos's paper
- isomiRs::mirna_ex_rseData frame containing mirna expression data
- iterativeBMA::testClassSample Test Data for the Iterative BMA Algorithm
- iterativeBMA::testDataSample Test Data for the Iterative BMA Algorithm
- iterativeBMA::trainClassSample Training Data for the Iterative BMA Algorithm
- iterativeBMA::trainDataSample Training Data for the Iterative BMA Algorithm
- iterativeBMAsurv::testCensSample Test Data for the Iterative BMA Algorithm for Survival Analysis
- iterativeBMAsurv::testDataSample Test Data for the Iterative BMA Algorithm for Survival Analysis
- iterativeBMAsurv::testSurvSample Test Data for the Iterative BMA Algorithm for Survival Analysis
- iterativeBMAsurv::trainCensSample Training Data for the Iterative BMA Algorithm for Survival Analysis
- iterativeBMAsurv::trainDataSample Training Data for the Iterative BMA Algorithm for Survival Analysis
- iterativeBMAsurv::trainSurvSample Training Data for the Iterative BMA Algorithm for Survival Analysis
- IVAS::sampleexpCEU expression data
- IVAS::samplesnpCEU genotype data
- IVAS::samplesnplocussnplocus
- ivygapSE::ivySEivySE: SummarizedExperiment for IvyGAP expression data and metadata
- IWTomics::ETn_exampleETn Recombination hotspots data
- IWTomics::features_exampleExample of features
- IWTomics::regionsFeatures_centerExample of '"IWTomicsData"' object with center alignment
- IWTomics::regionsFeatures_scaleExample of '"IWTomicsData"' object with scale alignment
- IWTomics::regions_exampleExample of regions
- KBoost::D4_multi_1Dream 4 multifactorial pertubation challenge dataset 1
- KBoost::D4_multi_2Dream 4 multifactorial pertubation challenge dataset 2
- KBoost::D4_multi_3Dream 4 multifactorial pertubation challenge dataset 3
- KBoost::D4_multi_4Dream 4 multifactorial pertubation challenge dataset 4
- KBoost::D4_multi_5Dream 4 multifactorial pertubation challenge dataset 5
- KBoost::G_D4_multi_1Gold Standard Dream 4 multifactorial pertubation challenge dataset 1
- KBoost::G_D4_multi_2Gold Standard Dream 4 multifactorial pertubation challenge dataset 2
- KBoost::G_D4_multi_3Gold Standard Dream 4 multifactorial pertubation challenge dataset 3
- KBoost::G_D4_multi_4Gold Standard Dream 4 multifactorial pertubation challenge dataset 4
- KBoost::G_D4_multi_5Gold Standard Dream 4 multifactorial pertubation challenge dataset 5
- KBoost::Gerstein_Prior_ENET_2Gene Regulatory Network from human ChIP-Seq data in Encode
- KBoost::Human_TFsIndex of human genes' Symbols, Entrez and Ensembl for K-Boost Pacakge that correspond to transcription factors.
- KBoost::IRMA_GoldIRMA Gold Standard Network
- KBoost::irma_offIRMA Off Dataset
- KBoost::irma_onIRMA On Dataset
- KCsmart::hsMirrorLocsMirror locations of the human genome
- KCsmart::hsSampleDataHomo Sapiens artificial cgh data set
- KCsmart::mmMirrorLocsMirror locations of the mouse genome
- kebabs::ccannotKeBABS Sequence Data
- kebabs::ccgroupsKeBABS Sequence Data
- kebabs::ccseqKeBABS Sequence Data
- kebabs::enhancerFBKeBABS Sequence Data
- kebabs::yCCKeBABS Sequence Data
- kebabs::yFBKeBABS Sequence Data
- kebabs::yMCKeBABS Sequence Data
- kebabs::yRegKeBABS Sequence Data
- KEGGgraph::KEGGEdgeSubtypeKEGG edge subtypes
- KEGGgraph::KEGGEdgeTypeKEGG edge types
- KEGGgraph::KEGGNodeTypeKEGG node types
- KEGGgraph::KEGGPATHID2NAMEKEGG pathway identifier to name
- keggorthology::KOgraphcreate a graph from a specific data frame format for KEGG orthology
- keggorthology::keggOrthDFcreate a graph from a specific data frame format for KEGG orthology
- KinSwingR::example_phosphoproteomeExample phosphoproteome.
- KinSwingR::phosphositeplus_humanHuman kinase-substrates derived from PhosphositePlus.
- LACE::inferenceResults obtained with the function LACE on the provided input data from Rambow, Florian, et al. "Toward minimal residual disease-directed therapy in melanoma." Cell 174.4 (2018): 843-855.
- LACE::longitudinal_sc_variantsMutation data from Rambow, Florian, et al. "Toward minimal residual disease-directed therapy in melanoma." Cell 174.4 (2018): 843-855.
- LBE::golub.pvalp-values corresponding to the gene expression data from Golub et al. (1999).
- LBE::hedenfalk.pvalp-values corresponding to the gene expression data from Hedenfalk et al. (2001).
- ldblock::EUR_singletonssingletons from EUR
- ldblock::sampinf_1kgpopulation and relationship information for 1000 genomes
- LEA::example_ancestrymap'ancestrymap' format description
- LEA::example_genoInput file for 'snmf'
- LEA::example_lfmmInput file for 'lfmm'
- LEA::example_ped'ped' format description
- LEA::example_vcf'vcf' format description
- LEA::offset_exampleExample data for genetic offset analysis
- LEA::tutorialExample tutorial data sets
- LedPred::crm.featuresThis is data to be included in my package
- LedPred::feature.rankingThis is data to be included in my package
- lefser::zeller14Example dataset for lefser
- lemur::glioblastoma_example_dataThe 'glioblastoma_example_data' dataset
- les::exprsSpike-in ChIP-chip data set
- les::posSpike-in ChIP-chip data set
- les::pvalSpike-in ChIP-chip data set
- les::referenceSpike-in ChIP-chip data set
- lfa::hgdp_subsetHGDP subset
- limpca::UCHUCH: the Urine Citrate-Hippurate metabolomic dataset
- limpca::trouttrout: the Rainbow trouts transcriptomic dataset
- LinkHD::RuminotypesWhole Ruminotypes dataset communities
- LinkHD::TaraoceansTARA Oceans datasets
- Linnorm::Islam2011scRNA-seq data from Islam et al. 2011
- Linnorm::LIHCPartial RNA-seq data from TCGA LIHC (Liver Hepatocellular Carcinoma)
- Linnorm::SEQCPartial RNA-seq data from SEQC/MAQC-III Sample A
- LinTInd::cellsinfoexample of cellsinfo
- LinTInd::celltypeexample of celltype
- LinTInd::cutsiteexample of cutsite
- LinTInd::dataexample of data
- LinTInd::refexample of ref
- LinTInd::scarformexample of scarform
- LinTInd::scarinfoexample of scarinfo
- LinTInd::scarrefexample of scarref
- LinTInd::scarref_allexample of scarref_all
- LinTInd::tagexample of tag
- LinTInd::treeinfoexample of treeinfo
- lionessR::expOS data
- lionessR::targetsOS data
- lipidr::data_normalizedExample dataset (normalized and log2 transformed)
- lipidr::lipidDefaultsDefault values for lipidr internal functions A set of default mappings and annotation used internally to correctly parse lipid molecule names.
- lipidr::lipidnames_patternPatterns used in parsing lipid names
- LOBSTAHS::default.LOBdbaseLOBSTAHS default databases and database generation parameters
- LOBSTAHS::default.acylRangesLOBSTAHS default databases and database generation parameters
- LOBSTAHS::default.adductHierarchiesLOBSTAHS default databases and database generation parameters
- LOBSTAHS::default.componentCompTableLOBSTAHS default databases and database generation parameters
- LOBSTAHS::default.oxyRangesLOBSTAHS default databases and database generation parameters
- LOBSTAHS::default.rt.windowsLOBSTAHS default databases and database generation parameters
- loci2path::biocartaeQTL geneset enrichment query demo data
- loci2path::eset.listeQTL geneset enrichment query demo data
- loci2path::query.greQTL geneset enrichment query demo data
- logicFS::cl.logicfsExample Data of logicFS
- logicFS::data.logicfsExample Data of logicFS
- LOLA::userSetsAn example set of regions, sampled from the example database.
- LOLA::userUniverseA reduced GRanges object from the example regionDB database
- LPE::LeyGene Expression Data from Mouse Immune response study, (2002)
- lpNet::dat.normalized
- lpNet::dat.unnormalized
- LRcell::example_LRcell_resAn example output of LRcell using data example_gene_pvals and mouse_FC_marker_genes.
- LRcell::example_gene_pvalsExample gene_pvals named vector from mouse experiment.
- LRcell::mouse_FC_marker_genesExample marker genes from mouse FC brain region.
- LRcell::mouse_celltypesMapping between subclusters and cell types in Mouse Brain
- lumi::example.lumiExample Illumina Expression data in LumiBatch class
- lumi::example.lumiMethyExample Illumina Infinium Methylation data in MethyLumiM class
- lumi::example.methyTitrationExample Illumina Infinium Methylation titration data in MethyLumiM class
- M3C::desxGBM clinical annotation data
- M3C::mydataGBM expression data
- maCorrPlot::datA.ampExample data for package maCorrSample
- maCorrPlot::datA.mas5Example data for package maCorrSample
- maCorrPlot::datA.rmaExample data for package maCorrSample
- maCorrPlot::datB.ampExample data for package maCorrSample
- maCorrPlot::datB.mas5Example data for package maCorrSample
- maCorrPlot::datB.rmaExample data for package maCorrSample
- made4::NCI60Microarray gene expression profiles of the NCI 60 cell lines
- made4::khanMicroarray gene expression dataset from Khan et al., 2001. Subset of 306 genes.
- MADSEQ::aneuploidy_chr18An S4 class MadSeq object
- magpie::power.testPower calculation results for GSE46705
- magpie::power.testPower calculation results for GSE46705
- magpie::power.testPower calculation results for GSE46705
- magpie::power.testPower calculation results for GSE46705
- magpie::power.testPower calculation results for GSE46705
- magpie::power.testPower calculation results for GSE46705
- magrene::gma_grnSample soybean GRN
- magrene::gma_paralogsSoybean (Glycine max) duplicated genes
- magrene::gma_ppiSample soybean PPI network
- magrene::nullsNull distribution of motif frequencies for vignette data set
- MAI::untargeted_LCMS_dataExample data set containing missing values
- MAIT::DatabaseHuman Metabolome Database
- MAIT::MAITMAIT
- MAIT::biotransformationsTablebiotransformationsTable
- MAIT::negAdductsNegative adducts table
- MAIT::posAdductsPositive adducts table
- MANOR::SNR.flagExamples of flag objects to apply to CGH arrays
- MANOR::amplicon.flagExamples of flag objects to apply to CGH arrays
- MANOR::chromosome.flagExamples of flag objects to apply to CGH arrays
- MANOR::clone.qscoreExamples of qscore objects (quality scores) to apply to CGH arrays
- MANOR::control.flagExamples of flag objects to apply to CGH arrays
- MANOR::dapi.snr.flagExamples of flag objects to apply to CGH arrays
- MANOR::dyn.x.qscoreExamples of qscore objects (quality scores) to apply to CGH arrays
- MANOR::dyn.y.qscoreExamples of qscore objects (quality scores) to apply to CGH arrays
- MANOR::dynamics.qscoreExamples of qscore objects (quality scores) to apply to CGH arrays
- MANOR::edgeExamples of array-CGH data with spatial artifacts
- MANOR::edge.normExamples of array-CGH data with spatial artifacts
- MANOR::global.spatial.flagExamples of flag objects to apply to CGH arrays
- MANOR::gradientExamples of array-CGH data with spatial artifacts
- MANOR::gradient.normExamples of array-CGH data with spatial artifacts
- MANOR::intensity.flagExamples of flag objects to apply to CGH arrays
- MANOR::local.spatial.flagExamples of flag objects to apply to CGH arrays
- MANOR::num.chromosome.flagInternal Functions for MANOR Package
- MANOR::pct.clone.qscoreExamples of qscore objects (quality scores) to apply to CGH arrays
- MANOR::pct.replicate.qscoreExamples of qscore objects (quality scores) to apply to CGH arrays
- MANOR::pct.spot.before.qscoreExamples of qscore objects (quality scores) to apply to CGH arrays
- MANOR::pct.spot.qscoreExamples of qscore objects (quality scores) to apply to CGH arrays
- MANOR::position.flagExamples of flag objects to apply to CGH arrays
- MANOR::ref.snr.flagExamples of flag objects to apply to CGH arrays
- MANOR::rep.flagExamples of flag objects to apply to CGH arrays
- MANOR::replicate.auxInternal Functions for MANOR Package
- MANOR::replicate.flagExamples of flag objects to apply to CGH arrays
- MANOR::smoothness.qscoreExamples of qscore objects (quality scores) to apply to CGH arrays
- MANOR::spatial.flagExamples of flag objects to apply to CGH arrays
- MANOR::spot.corr.flagInternal Functions for MANOR Package
- MANOR::spot.flagExamples of flag objects to apply to CGH arrays
- MANOR::unique.flagExamples of flag objects to apply to CGH arrays
- MANOR::val.mark.flagExamples of flag objects to apply to CGH arrays
- MANOR::var.replicate.qscoreExamples of qscore objects (quality scores) to apply to CGH arrays
- MantelCorr::GolubTrainGolub Training Set
- MAPFX::ord.fcs.raw.meta.df.out_ffcMetadata of the example MPC data
- MAPFX::ord.fcs.raw.meta.df.out_mpcMetadata of the example FFC data
- MAPFX::ord.fcs.raw.mt_ffcSubset of the single-cell murine lung data at steady state from an MPC experiment
- MAPFX::ord.fcs.raw.mt_mpcSubset of the sorted CD4+ and CD8+ T cells from mice splenocytes from an FFC experiment
- marr::msprepCOPDExample of processed mass spectrometry dataset
- marray::swirlGene expression data from Swirl zebrafish cDNA microarray experiment
- martini::minigwasDescription of the minigwas dataset.
- martini::minippiPPIs for the minigwas dataset.
- martini::minisnpMappingGenes for the minigwas dataset.
- maSigPro::ISOdataRNA-Seq dataset example for isoforms
- maSigPro::ISOdesignExperimental design for ISOdata dataset example
- maSigPro::NBdataRNA-Seq dataset example
- maSigPro::NBdesignExperimental design for RNA-Seq example
- maSigPro::data.abioticGene expression data potato abiotic stress
- maSigPro::edesign.abioticExperimental design potato abiotic stress
- maSigPro::edesignCTExperimental design with a shared time
- maSigPro::edesignDRExperimental design with different replicates
- maskBAD::exmaskOutput object of the function mask
- maskBAD::newAffyBatchAffyBatch with reduced genes
- maskBAD::newCdfObject of type environment
- maskBAD::sequenceMaskObject containing sequence information for probes.
- MassArray::MassArray.example.dataMassArray Data object
- massiR::massi.esetmassi.eset
- massiR::massi.test.datasetThe massi test dataset
- massiR::massi.test.probesThe massi test probes
- massiR::y.probesY chromosome probe list
- MassSpecWavelet::exampleMSAn example mass spectrum
- MAST::maitsMAITs data set, RNASeq
- MAST::predicted_sigPredicted signatures
- MAST::vbetaVbeta Data Set
- MAST::vbetaFAVbeta Data Set, FluidigmAssay
- mastR::ccle_crc_5RNA-seq TPM data of 5 CRC cell line samples from CCLE.
- mastR::im_data_6RNA-seq TMM normalized counts data of 6 sorted immune subsets.
- mastR::lm22LM22 matrix for CIBERSORT.
- mastR::lm7LM7 matrix for CIBERSORT.
- mastR::msigdb_gobp_nkSub-collection of MSigDB gene sets.
- mastR::nk_markersNK cell markers combination.
- matchBox::matchBoxExpressionExample data: ranking from three differential gene expression experiments
- MBCB::expressionSignalMBCB - Bayesian Background Correction for Illumina Beadarray
- MBCB::negativeControlMBCB - Bayesian Background Correction for Illumina Beadarray
- MBECS::dummy.listMock-up microbiome abundance table and meta-data.
- MBECS::dummy.mbecMock-up microbiome abundance table and meta-data.
- MBECS::dummy.psMock-up microbiome abundance table and meta-data.
- mBPCR::jekoChr11Array250KnspAffymetrix GeneChip Mapping 250K NSP Array data of JEKO-1 cell line (chr. 11)
- mBPCR::rec10kAffymetrix GeneChip Mapping 10K Array data of REC-1 cell line
- mbQTL::CovFile'mbQTL' "CovFile"
- mbQTL::SnpFile'mbQTL' "SnpFile"
- mbQTL::metagenomeSeqObj'mbQTL' "metagenomeSeqObj" "MetagenomSeqObj" is an 'MRexperiment' object format of the "microbeAbund" file.
- mbQTL::microbeAbund'mbQTL' "microbiomeAbund" File
- MBttest::datThe Transcriptomic data and t-test results.
- MBttest::jkttcellJurkat T-cell Transcritomic Data
- MBttest::skjtSimulated Null Transcriptomic data
- MCbiclust::CCLE_samplesClinical information for CCLE data
- MCbiclust::CCLE_smallSubset of expression levels of CCLE data
- MCbiclust::Mitochondrial_genesList of known mitochondrial genes
- mCSEA::exprTestExpression data example
- mCSEA::myRankPrecomputed mCSEA results
- mCSEA::myResultsPrecomputed mCSEA results
- mdp::example_dataExpression data example
- mdp::example_phenoPhenotypic data example
- mdp::sample_dataSample score results
- mdqc::allQCQC report for MLL.B
- MEAT::CpGs_in_MEATDescription of the CpGs used in MEAT
- MEAT::CpGs_in_MEAT2.0Description of the CpGs used in MEAT2.0
- MEAT::GSE121961GSE121961 methylation data
- MEAT::GSE121961_phenoGSE121961 phenotypes
- MEAT::elasticnet_model_MEATElastic net model used in the original muscle clock (MEAT).
- MEAT::elasticnet_model_MEAT2.0Elastic net model used in the updated muscle clock (MEAT 2.0).
- MEAT::gold.mean.MEATMean methylation in dataset GSE50498 reduced to the 19,401 CpGs of MEAT
- MEAT::gold.mean.MEAT2.0Mean methylation in dataset GSE50498 reduced to the 18,747 CpGs of MEAT 2.0
- MEB::real_data_dspA real dataset of genes between the different species.
- MEB::real_data_spA real dataset of genes between the same species.
- MEB::sim_data_dspA simulation dataset of genes between the differetn species.
- MEB::sim_data_spA simulation dataset of genes between the same species.
- MEB::sim_scRNA_dataA simulation scRNA-seq dataset from splatter package.
- MEB::stable_geneThe name of the stable genes in all dataset.
- MEDME::testMEDMEsetDataset of class MEDMEset for testing MEDME
- MEIGOR::cnolistA CNOlist from CellNOptR paclage
- MEIGOR::cnolistA CNOlist from CellNOptR paclage
- MEIGOR::cnolistA CNOlist from CellNOptR paclage
- MEIGOR::cnolist_cellnoptA CNOlist from CellNOptR paclage
- MEIGOR::modelA model from CellNoptR
- MEIGOR::modelA model from CellNoptR
- MEIGOR::modelA model from CellNoptR
- MEIGOR::model_cellnoptA model from CellNoptR
- MEIGOR::paramsOptOptimal parameters for simulation with CNORode
- Melissa::melissa_encode_dtSynthetic ENCODE single cell methylation data
- Melissa::melissa_synth_dtSynthetic single cell methylation data
- memes::example_ameExample runAme() output
- memes::example_ame_largerunAme() output for example_chip_summits split by binding description
- memes::example_chip_summitsAnnotated Transcription Factor ChIP-seq summits
- memes::example_dremeExample runDreme() output
- memes::example_dreme_by_bindingrunDreme() output for example_chip_summits split by binding description
- memes::example_dreme_tomtomExample runDreme() output after passing to runTomTom()
- memes::example_fimoExample runFimo() output
- memes::example_peaksExample ChIP-seq peaks
- memes::example_rnaseqRNAseq data from Early and Late Drosophila wings
- memes::example_tomtomExample runTomTom() output
- Mergeomics::job.kdaKey Driver Analyzing results
- meshes::hsamdDATA Sets
- meshes::meshtblDATA Sets
- messina::kirc.exprsExample TCGA KIRC RNAseq expression and survival data
- messina::kirc.survExample TCGA KIRC RNAseq expression and survival data
- metabCombiner::metabBatchesThree LC-MS Metabolomics Batch Datasets
- metabCombiner::plasma2020 minute LC-MS Analysis of Human Plasma
- metabCombiner::plasma3030 minute LC-MS Analysis of Human Plasma
- metabomxtr::euMetabCDataA sample data set of truncated metabolomics data.
- metabomxtr::euMetabDataA sample data set of truncated metabolomics data.
- metabomxtr::metabdataA sample data set of truncated metabolomics data
- MetaboSignal::MetaboSignal_tableExample of MetaboSignal network-table
- MetaboSignal::directionality_reactionsList of KEGG reactions with incorrect/inconsistent directionality
- MetaboSignal::hpaNormalTissueExpression profiles for proteins in human tissues
- MetaboSignal::keggNet_exampleKEGG network example
- MetaboSignal::kegg_pathwaysExamples of metabolic and signaling human KEGG pathways
- MetaboSignal::mergedNet_exampleNetwork containing KEGG, OmniPath and TRRUST interactions
- MetaboSignal::ppiNet_exampleSignaling-transduction network
- MetaboSignal::regulatory_interactionsRegulatory interactions from OmniPath and TRRUST
- metaCCA::N1Number of individuals in study 1.
- metaCCA::N2Number of individuals in study 2.
- metaCCA::S_XX_study1Correlations between 10 SNPs corresponding to the population underlying study 1.
- metaCCA::S_XX_study2Correlations between 10 SNPs corresponding to the population underlying study 2.
- metaCCA::S_XY_full_study1Univariate summary statistics of 10 traits across 1000 SNPs (study 1).
- metaCCA::S_XY_full_study2Univariate summary statistics of 10 traits across 1000 SNPs (study 2).
- metaCCA::S_XY_study1Univariate summary statistics of 10 traits across 10 SNPs (study 1).
- metaCCA::S_XY_study2Univariate summary statistics of 10 traits across 10 SNPs (study 2).
- metagenomeSeq::lungDataOTU abundance matrix of samples from a smoker/non-smoker study
- metagenomeSeq::mouseDataOTU abundance matrix of mice samples from a diet longitudinal study
- metahdep::HGU.DifExp.listHGU.DifExp.list: A list of 4 ES.obj objects
- metahdep::HGU.newnamesHGU.newnames
- metahdep::HGU.prep.listHGU.prep.list
- metahdep::gloss.Table1gloss: Data from the JEBS glossing paper
- metahdep::gloss.Vgloss: Data from the JEBS glossing paper
- metahdep::gloss.Xgloss: Data from the JEBS glossing paper
- metahdep::gloss.thetagloss: Data from the JEBS glossing paper
- metaMS::DBInformation on three chemical standards measured in GC-MS (liquid injection)
- metaMS::GCresultsResults of metaMS for a small GC-MS data set
- metaMS::LCDBtestSample DB for LC-MS annotation
- metaMS::LCresultsResult metaMS for a small LC-MS data set
- metaMS::Orbitrap.RPExample settings for 'metaMS'
- metaMS::Synapt.NPExample settings for 'metaMS'
- metaMS::Synapt.RPExample settings for 'metaMS'
- metaMS::TSQXLS.GCExample settings for 'metaMS'
- metaMS::errfMass error surface for Waters Synapt Q-TOF spectrometers
- metaMS::exptableSample table for the generation of a database of standards (LCMS)
- metaMS::smallDBInformation on three chemical standards measured in GC-MS (liquid injection)
- metaMS::stdInfoInformation on three chemical standards measured in GC-MS (liquid injection)
- MetaNeighbor::GOhumanGOhuman
- MetaNeighbor::GOmouseGOmouse
- MetaNeighbor::mn_datamn_data
- metapone::hmdbCompMZthe m/z values of common adduct ions of HMDB metaboites
- metapone::hmdbCompMZ.metaponethe m/z values of common adduct ions of metapone metaboites
- metapone::negExample negative mode data from the Metabolome Atlas of the Aging Mouse Brain
- metapone::paPathway-metabolite match file.
- metapone::posExample positive mode data from the Metabolome Atlas of the Aging Mouse Brain
- metaSeq::BreastCancerMultiple RNA-Seq count data designed as Breast Cancer cell lines vs Normal cells
- metaSeq::Result.MetaResult of meta.oneside.noiseq against Brast Cancer data
- metaSeq::StudyACount data of SRP008746
- metaSeq::pvalsP-values or probability calculated by DESeq, edgeR, baySeq, NOISeq, and DEGseq against StudyA
- metaSeq::text.busca_unixOne of C++ re-implimated components in NOISeq
- metaSeq::text.busca_winOne of C++ re-implimated components in NOISeq
- metaSeq::text.n.menor_unixOne of C++ re-implimated components in NOISeq
- metaSeq::text.n.menor_winOne of C++ re-implimated components in NOISeq
- metaseqR2::hg19pvaluesp-values from human RNA-Seq data with two conditions, four samples
- metaseqR2::libsizeListMm9Mouse RNA-Seq data with two conditions, four samples
- metaseqR2::mm9GeneCountsMouse RNA-Seq data with two conditions, four samples
- metaseqR2::sampleListMm9Mouse RNA-Seq data with two conditions, four samples
- MetCirc::compartmentTissueExample data for 'MetCirc': 'compartmentTissue'
- MetCirc::convertExampleDFExample data for 'MetCirc': convertExampleDF
- MetCirc::msp2spectraExample data for 'MetCirc': 'msp2spectra'
- MetCirc::sd01_outputXCMSExample data for 'MetCirc': 'sd01_outputXCMS'
- MetCirc::sd02_deconvolutedExample data for 'MetCirc': sd02_deconvoluted
- MetCirc::similarityMatExample data for 'MetCirc': 'similarityMat'
- MetCirc::sps_tissueExample data for 'MetCirc': 'sps_tissue'
- MetCirc::tissueExample data for 'MetCirc': 'tissue'
- methimpute::arabidopsis_TEsTransposable element coordinates for Arabidopsis (chr1)
- methimpute::arabidopsis_chromosomesChromosome lengths for Arabidopsis
- methimpute::arabidopsis_genesGene coordinates for Arabidopsis (chr1)
- methimpute::arabidopsis_toydataToy data for Arabidopsis (200.000bp of chr1)
- methInheritSim::dataSimExampleA 'list' containing methylation information used by some internal functions (for demo purpose.
- methInheritSim::samplesForChrSyntheticAll samples information, formated by 'methylKit', in a 'methylBase' format (for demo purpose).
- methodical::TumourMethDatasetsTumourMethDatasets
- methodical::hg38_cpgs_subsethg38_cpgs_subset
- methodical::infinium_450k_probe_granges_hg19infinium_450k_probe_granges_hg19
- methodical::tubb6_correlation_plottubb6_correlation_plot
- methodical::tubb6_cpg_meth_transcript_corstubb6_cpg_meth_transcript_cors
- methodical::tubb6_meth_rsetubb6_meth_rse
- methodical::tubb6_tmrstubb6_tmrs
- methodical::tubb6_transcript_countstubb6_transcript_counts
- methodical::tubb6_tsstubb6_tss
- MethPed::MethPed_900probesList of 900 probes in the predictor data
- MethPed::MethPed_sampleSample dataset to MethPed package.
- MethReg::clinicalTCGA-COAD clinical matrix for 38 samples retrieved from GDC using TCGAbiolinks
- MethReg::dna.met.chr21TCGA-COAD DNA methylation matrix (beta-values) for 38 samples (only chr21) retrieved from GDC using TCGAbiolinks
- MethReg::gene.exp.chr21.log2TCGA-COAD gene expression matrix (log2 (FPKM-UQ + 1)) for 38 samples (only chromosome 21) retrieved from GDC using TCGAbiolinks
- methrix::methrix_dataWGBS for colon cancer, chr21 and chr22
- MethylAid::exampleDatasummarizedData object on 500 450k Human Methylation samples
- methylCC::FlowSorted.Blood.450k.subA reduced size of the FlowSorted.Blood.450k dataset
- methylCC::offMethRegionsUnmethylated regions for all celltypes
- methylCC::onMethRegionsMethylated regions for all celltypes
- methylclock::progress_dataPROGRESS cohor data
- methylclock::progress_varsPROGRESS cohort variables
- methylGSA::CpG2GeneAn example of user user-supplied mapping between CpGs and genes
- methylGSA::GS.listAn example of user input gene sets
- methylGSA::cpg.pvalAn example of user input cpg.pval
- methyLImp2::betaA subset of GSE199057 dataset for vignette demonstration
- methyLImp2::beta_metaMetadata information for GSE199057 dataset for vignette demonstration
- methylInheritance::demoForTransgenerationalAnalysisThe methylation information from samples over three generations. Information for each generation is stored in a 'methylRawList' format (for demo purpose).
- methylInheritance::methylInheritanceResultsAll observed and permutation results formatted in a 'methylInheritanceResults' class (for demo purpose).
- methylInheritance::samplesForTransgenerationalAnalysisAll samples information, formated by 'methylKit', in a 'methylRawList' format (for demo purpose).
- methylKit::methylBase.objExample methylBase object.
- methylKit::methylDiff.objExample methylKit objects.
- methylKit::methylRawList.objExample methylRawList object.
- MethylMix::BatchDataBatchData data set
- MethylMix::GEcancerCancer Gene expression data of glioblastoma patients from the TCGA project
- MethylMix::METcancerDNA methylation data from cancer tissue from glioblastoma patients from the TCGA project
- MethylMix::METnormalDNA methylation data from normal tissue from glioblastoma patients
- MethylMix::ProbeAnnotationProbeAnnotation data set
- MethylMix::SNPprobesSNPprobes data set
- methylscaper::human_bmHuman gene symbols and positions
- methylscaper::mouse_bmMouse gene symbols and positions
- methylscaper::reads_smExample reads from single-molecule experiment
- methylscaper::ref_seqExample reference sequence to align reads to from a single-molecule experiment
- methylscaper::singlecell_subsetExample preprocessed single-cell experiment subset
- methylscaper::singlemolecule_exampleExample preprocessed single-molecule experiment
- methylSig::bsseq_destrandedBSseq object read from destranded coverage files
- methylSig::bsseq_multichromBSseq object with loci on multiple chromosomes
- methylSig::bsseq_strandedBSseq object read from stranded coverage files
- methylSig::promoters_grGRanges object with collapsed promoters on chr21 and chr22
- methylumi::CpGsData frame describing loci on the 27 and 450k arrays.
- methylumi::mldatExample SAM format Illumina methylation dataset
- MetID::InchiKeyInchikey database.
- MetID::demo1Example of input dataset, in which colnames does not meet requirement.
- MetID::demo2Example of input dataset, in which colnames does not meet requirement.
- MetID::kegg_networkPairs of kegg network.
- MetNet::mat_testExample data for 'MetNet': unit tests
- MetNet::mat_test_zExample data for 'MetNet': unit tests
- MetNet::peaklistExample data for 'MetNet': data input
- MetNet::sps_subSpectra data to test addSpectralSimilarity
- MetNet::x_annotationExample annotation for 'MetNet': data input
- MetNet::x_testExample data for 'MetNet': data input
- Mfuzz::yeastGene expression data of the yeast cell cycle
- Mfuzz::yeast.tableGene expression data of the yeast cell cycle as table
- Mfuzz::yeast.table2Gene expression data of the yeast cell cycle as table
- MGFM::ds2.matMicroarray gene expression data set
- MGFR::ref.matRNA-seq gene expression data set
- mgsa::example_goExample GO sets for mgsa
- mgsa::example_oExample objects for mgsa
- mia::GlobalPatternsGlobal patterns of 16S rRNA diversity at a depth of millions of sequences per sample.
- mia::HintikkaXODataMultiomics dataset from 40 rat samples
- mia::Tengeler2020Gut microbiota profiles of 27 individuals with ADHD and healthy controls
- mia::Tito2024QMPFecal microbiota samples from 589 patients across different colorectal cancer stages
- mia::dmn_seTwins' microbiome data from 278 individuals
- mia::enterotypeHuman gut microbiome dataset from 22 subjects based on shotgun DNA sequencing
- mia::esophagusHuman esophageal community from 3 individuals
- mia::peerj13075Skin microbial profiles 58 genetically unrelated individuals
- miaViz::col_graphmiaViz example data
- miaViz::row_graphmiaViz example data
- miaViz::row_graph_ordermiaViz example data
- microbiome::atlas1006HITChip Atlas with 1006 Western Adults
- microbiome::dietswapDiet Swap Data
- microbiome::hitchip.taxonomyHITChip Taxonomy
- microbiome::peerj32Probiotics Intervention Data
- microbiomeMarker::caporaso16S rRNA data from "Moving pictures of the human microbiome"
- microbiomeMarker::cid_ying16S rRNA data of 94 patients from CID 2012
- microbiomeMarker::ecamData from Early Childhood Antibiotics and the Microbiome (ECAM) study
- microbiomeMarker::enterotypes_arumugamEnterotypes data of 39 samples
- microbiomeMarker::kostic_crcData from a study on colorectal cancer (kostic 2012)
- microbiomeMarker::oxygenOxygen availability 16S dataset, of which taxa table has been summarized for python lefse input
- microbiomeMarker::pediatric_ibdIBD stool samples
- microbiomeMarker::spontaneous_colitisThis is a sample data from lefse python script, a 16S dataset for studying the characteristics of the fecal microbiota in a mouse model of spontaneous colitis.
- MicrobiomeProfiler::Psoriasis_dataExample data: a vector of 134 significantly different functional COGs between Psoriasis patients and controls
- MicrobiomeProfiler::Rat_dataExample data: a vector of 91 KEGG Orthologies (KOs) showing significant associations with weaning weight
- MicrobiomeProfiler::microbiota_taxlistExample data: a vector of 54 bacterial genera tested for significantly between T2D metformin samples
- MicrobiotaProcess::hmp_aerobiosis_small(Data) Small subset of the HMP 16S dataset
- MicrobiotaProcess::kostic2012crc(Data) Genomic analysis identifies association of Fusobacterium with colorectal carcinoma (2012)
- MicrobiotaProcess::mouse.time.mpse(Data) An example data
- MicrobiotaProcess::test_otu_data(Data) simulated dataset.
- microRNA::hsSeqsHuman Mature microRNA Sequences
- microRNA::hsTargetsHuman microRNAs and their target IDs
- microRNA::mmSeqsMouse Mature microRNA Sequences
- microRNA::mmTargetsMouse microRNAs and their target IDs
- microRNA::s3utrTest sequence data
- microSTASIS::clrDetected ASV from multiple individuals at four different sampling times.
- MICSQTL::seExample data
- midasHLA::MiDAS_tut_HLAMiDAS tutorial HLA data
- midasHLA::MiDAS_tut_KIRMiDAS tutorial KIR data
- midasHLA::MiDAS_tut_objectMiDAS tutorial MiDAS object
- midasHLA::MiDAS_tut_phenoMiDAS tutorial phenotype data
- midasHLA::allele_frequenciesAlleles frequencies scraped from allelefrequencies.net
- midasHLA::dict_dist_granthamGrantham distance
- midasHLA::kir_frequenciesKIR genes frequencies scraped from allelefrequencies.net
- miloR::sim_discretesim_discrete
- miloR::sim_familysim_family
- miloR::sim_nbglmmsim_nbglmm
- miloR::sim_trajectorySimulated linear trajectory data
- mina::hmp_desDesign file for HMP project, including 2711 samples in total.
- mina::hmp_otuOTU table of HMP project, data downloaded from https://www.hmpdacc.org/hmp/HMQCP/
- mina::maizeInternal testing data of maize project, vegetative stage samples only, including quantitative table (maize_asv.rds) and descriptive table (maize_des.txt) for testing.
- mina::maize_asvASV table of maize project, vegetative stage samples only.
- mina::maize_asv2Subset of ASV table of maize project, ASVs appear in less than 100 samples were filtered for later analysis.
- mina::maize_desDesign file of maize project, vegetative stage samples only, including 528 samples in total.
- mina::maize_des2Subset of design file of maize project, 313 samples are included.
- MineICA::icaSetCarbayoIcaSet-object containing a FastICA decomposition of gene expression microarrray-based data of bladder cancer samples.
- minet::syn.dataSimulated Gene Expression Data
- minet::syn.netSynTReN Source Network
- MinimumDistance::md_expAn example 'MinDistExperiment'
- MinimumDistance::md_grAn example 'MinDistGRanges' object
- MinimumDistance::trioSetListAn example 'TrioSetList' object
- MiPP::colonGene expression data for colon cancer
- MiPP::leuk1Gene expression data for leukemia
- MiPP::leuk2Gene expression data for leukemia
- miQC::metricsBasic scRNA-seq QC metrics from an ovarian tumor
- MIRA::bigBinDT1DNA methylation data for the "Applying MIRA to a Biological Question" vignette (1st part).
- MIRA::bigBinDT2DNA methylation data for the "Applying MIRA to a Biological Question" vignette (2nd part).
- MIRA::exampleAnnoDT1A data.table with annotation for a bisulfite sample.
- MIRA::exampleAnnoDT2Annotation data for the "Applying MIRA to a Biological Question" vignette.
- MIRA::exampleBSDTA data.table containing DNA methylation data.
- MIRA::exampleBSseqObjA small BSseq object.
- MIRA::exampleBinsA data.table with artificial binned methylation data
- MIRA::exampleRegionSetA Granges object with Nrf1-binding regions.
- MiRaGE::gene_expThis ExpressionSet represents gene expression of lung cancer cell line one day after let-7a transfection.
- miRBaseConverter::miRNATestDataset: miRNA Test Dataset
- miRcomp::lifetechThe processed data generated using the LifeTech software.
- miRcomp::qpcRb4The processed data generated using the 4 parameter sigmoidal method from the qpcR software.
- miRcomp::qpcRb5The processed data generated using the 5 parameter sigmodial method from the qpcR software.
- miRcomp::qpcRdefaultThe processed data generated using the default method (4 parameter log-logistic) implemented in the qpcR software package.
- miRcomp::qpcRl5The processed data generated using the 5 parameter log-logistic method from the qpcR software.
- miRcomp::qpcRlinexpThe processed data generated using the linear-exponential method implemented in the qpcR software package.
- mirIntegrator::GSE43592_mRNATop table of preprocessed mRNA of GSE43592 dataset.
- mirIntegrator::GSE43592_miRNATop table of preprocessed miRNA of GSE43592 dataset.
- mirIntegrator::augmented_pathwaysSignaling pathways augmented with miRNA.
- mirIntegrator::kegg_pathwaysList of KEGG signaling pathways of human.
- mirIntegrator::mirTarBaseMicroRNA-target interactions in human.
- mirIntegrator::names_pathwaysList of KEGG signaling pathways' names.
- MIRit::geneCountsCount matrix for gene expression in thyroid cancer
- MIRit::mirnaCountsCount matrix for microRNA expression in thyroid cancer
- miRNAmeConverter::example.miRNAsmiRNA names.
- miRNApath::mirnaobjmirnaobj, an S4 object of class "mirnapath"
- miRSM::BRCA_genesBRCA genes
- miRSM::ceRExpceRNA expression data
- miRSM::mRExpmRNA expression data
- miRSM::miRExpmiRNA expression data
- miRSM::miRTargetmiRNA-target ineractions
- mirTarRnaSeq::CombineThis is data is the mRNA expression across samples and miRNA expression data which is to be investigated in one file. This data set is used in documentation examples.
- mirTarRnaSeq::corr_0This is data is the mRNA FC and miRNA FC correlation data. This data set is used in documentation examples.
- mirTarRnaSeq::final_resultsThis is data is the mRNA FC and miRNA FC correlation/interaction data results after filteration. This data set is used in documentation examples.
- mirTarRnaSeq::geneVariantThis is data is the mRNA expression across samples and miRNA expression data which is to be investigated giving directions on which data is miRNA and which is mRNA. This data set is used in documentation examples.
- mirTarRnaSeq::inter0This is data is the mRNA FC and miRNA FC correlation/interaction original data. This data set is used in documentation examples.
- mirTarRnaSeq::mRNAThis is data is the mRNA expression file. This data set is used in documentation examples.
- mirTarRnaSeq::mRNA0_2This is data is the mRNA0_2 FC for 0-2 time point. This data set is used in documentation examples.
- mirTarRnaSeq::mRNA0_5This is data is the mRNA0_5 FC for 0-5 time point. This data set is used in documentation examples.
- mirTarRnaSeq::mRNA2_5This is data is the mRNA2_5 FC for 2-5 time point. This data set is used in documentation examples.
- mirTarRnaSeq::mRNA_fcThis is data is the combined mRNA FC for all time points. This data set is used in documentation examples.
- mirTarRnaSeq::mRNA_fc2This data is the mRNA fold change data set for difference or interrelation section. This data set is used in documentation examples.
- mirTarRnaSeq::miRNAThis is data is the miRNA expression file. This data set is used in documentation examples.
- mirTarRnaSeq::miRNA0_2This is data is the miRNA0_2 FC for 0-2 time point. This data set is used in documentation examples.
- mirTarRnaSeq::miRNA0_5This is data is the miRNA0_5 FC for 0-5 time point. This data set is used in documentation examples.
- mirTarRnaSeq::miRNA2_5This is data is the miRNA2_5 FC for 2-5 time point. This data set is used in documentation examples.
- mirTarRnaSeq::miRNA_fcThis is data is the combined miRNA FC for all time points. This data set is used in documentation examples.
- mirTarRnaSeq::miRNA_fc2This data is the miRNA fold change data set for difference or interrelation section. This data set is used in documentation examples.
- mirTarRnaSeq::miRandaThis is data is the results file from EBV miRanda getInputSpecies function. This data set is used in documentation examples.
- mirTarRnaSeq::miRandaMThis is data is the results file from mouse miRanda getInputSpecies function. This data set is used in documentation examples.
- mirTarRnaSeq::outsThis is data is the output file resulted from time point/conditions background correlation model. This data set is used in documentation examples.
- mirTarRnaSeq::outs2This is data is the output file resulted from time point/conditions background difference/interelation model. This data set is used in documentation examples.
- mirTarRnaSeq::resultsThis is data is the output file resulted from time point or conditions or correlation or interrelation model. This data set is used in documentation examples.
- mirTarRnaSeq::sig_InterRThis is data is the output file resulted from time point or conditions experiment for interrelation model after filtering and threshold modification. This data set is used in documentation examples.
- mirTarRnaSeq::sig_corrsThis is data is the output file resulted from time point or conditions experiment for correlation model after filtering and threshold modification. This data set is used in documentation examples.
- mirTarRnaSeq::some_modelThis is data is the results file from regression analysis and its estimates. This data set is used in documentation examples.
- missRows::NCI60Data of the NCI-60 Cell Lines with Missing Individuals
- mistyR::syntheticSynthetic benchmark data for mistyR
- mitch::genesetsExampleReactome gene sets
- mitch::k36aH3K36ac profile
- mitch::k9aH3K9ac profile
- mitch::myImportedDatamyImportedData: Example imported profiles
- mitch::myListmyList: A list of three edgeR results
- mitch::resExampleresExample: Example mitch result
- mitch::rnaRNA profile
- mitoClone2::M_P1Mitochondrial exclusionlist
- mitoClone2::M_P2Mitochondrial exclusionlist
- mitoClone2::N_P1Mitochondrial exclusionlist
- mitoClone2::N_P2Mitochondrial exclusionlist
- mixOmics::Koren.16S16S microbiome atherosclerosis study
- mixOmics::breast.TCGABreast Cancer multi omics data from TCGA
- mixOmics::breast.tumorsHuman Breast Tumors Data
- mixOmics::diverse.16S16S microbiome data: most diverse bodysites from HMP
- mixOmics::linnerudLinnerud Dataset
- mixOmics::liver.toxicityLiver Toxicity Data
- mixOmics::multidrugMultidrug Resistence Data
- mixOmics::nutrimouseNutrimouse Dataset
- mixOmics::srbctSmall version of the small round blue cell tumors of childhood data
- mixOmics::stemcellsHuman Stem Cells Data
- mixOmics::vac18Vaccine study Data
- mixOmics::vac18.simulatedSimulated data based on the vac18 study for multilevel analysis
- mixOmics::yeastYeast metabolomic study
- MLInterfaces::brennan_2013_tabS7excClinical characterization of 158 GBM samples from https://doi.org/10.1016/j.cell.2013.09.034 supp table S7
- MLSeq::cervicalCervical cancer data
- MMDiff2::Cfp1-PeaksPeaks for Cfp1-data set
- MMDiff2::MMDDBAmmd Object for Cfp1 example
- MMDiff2::mm9-Genesmm9-Genes
- MMUPHin::CRC_abdSpecies level feature abundance data of five public CRC studies
- MMUPHin::CRC_metaSample metadata of five public CRC studies
- MMUPHin::vaginal_abdSpecies level feature abundance data of two public vaginal studies
- MMUPHin::vaginal_metaSample metadata of two public vaginal studies
- mnem::appProcessed scRNAseq from pooled CRISPR screens
- moanin::testDataSmall data set for running examples
- moanin::testGenesGOSmall data set for running examples
- moanin::testMetaSmall data set for running examples
- mobileRNA::mRNA_datamRNA_data: simulated messenger RNA data for biological replicates
- mobileRNA::sRNA_datasRNA_data: simulated data for biological replicates
- MODA::datExpr1datExpr1
- MODA::datExpr2datExpr2
- ModCon::CodonsTable of codons and encoded amino acids
- ModCon::cdsCDS of firefly luciferase
- ModCon::hbgDonor sequences and their HBS
- ModCon::hexHexamers and Z scores
- Modstrings::MOD_RNA_DICT_MODOMICSModstrings internals
- Modstrings::MOD_RNA_DICT_TRNADBModstrings internals
- Modstrings::modsDNAModstrings internals
- Modstrings::modsRNAModstrings internals
- mogsa::NCI60_4array_supdatasupp data for Microarray gene expression profiles of the NCI 60 cell lines from 4 different platforms
- mogsa::NCI60_4arraysMicroarray gene expression profiles of the NCI 60 cell lines from 4 different platforms
- MoleculeExperiment::small_meA subsetted Xenium dataset include for demostration purposes.
- MOMA::example.gbm.maeGlioblastoma (GBM) Example Dataset
- MOMA::gbm.pathwaysGlioblastoma (GBM) Pathways
- MOMA::gene.mapGene Location Mapping
- MOMA::mutSigMutSig Blacklisted genes
- monocle::spike_dfSpike-in transcripts data.
- Moonlight2R::DEG_Methylation_AnnotationsOutput example from GMA function
- Moonlight2R::DEG_Mutations_AnnotationsDifferentially expressed genes's Mutations
- Moonlight2R::DEGsmatrixDifferentially expressed genes
- Moonlight2R::DiseaseListCancer-related biological processes
- Moonlight2R::EAGenesInformation about genes
- Moonlight2R::EncodePromotersPromoters
- Moonlight2R::EpiMix_Results_RegularOutput example from GMA function
- Moonlight2R::GEO_TCGAtabInformation on GEO and TCGA data
- Moonlight2R::LOC_proteinLevel of Consequence: Protein
- Moonlight2R::LOC_transcriptionLevel of Consequence: Transcription
- Moonlight2R::LOC_translationLevel of Consequence: Translation
- Moonlight2R::LUAD_sample_annoSample annotations of TCGA-LUAD project
- Moonlight2R::MetEvidenceDriverMethylation evidence table to define driver genes
- Moonlight2R::NCGNetwork of Cancer Genes 7.0
- Moonlight2R::Oncogenic_mediators_methylation_summaryOutput example from GMA function
- Moonlight2R::Oncogenic_mediators_mutation_summaryOncogenic Mediators Mutation Summary
- Moonlight2R::cscape_somatic_outputCscape-somatic annotations of TCGA-LUAD
- Moonlight2R::dataDMAOutput example from the function Driver Mutation Analysis
- Moonlight2R::dataFEAFunctional enrichment analysis
- Moonlight2R::dataFiltGene expression data from TCGA-LUAD
- Moonlight2R::dataGLSLiterature search of driver genes
- Moonlight2R::dataGMAOutput example from GMA function
- Moonlight2R::dataGRNGene regulatory network
- Moonlight2R::dataGRN_no_noiseGene regulatory network
- Moonlight2R::dataMAFMutation data from TCGA LUAD
- Moonlight2R::dataMethylMethylation data matrix from TCGA-LUAD project
- Moonlight2R::dataPRAOutput example from function Pattern Recognition Analysis
- Moonlight2R::dataURAUpstream regulator analysis
- Moonlight2R::dataURA_plotUpstream regulator analysis
- Moonlight2R::knownDriverGenesInformation of known cancer driver genes from COSMIC
- Moonlight2R::listMoonlightList of oncogenic mediators of 5 TCGA cancer types
- Moonlight2R::tabGrowBlockInformation of growing/blocking characteristics of 101 biological processes
- MoonlightR::DEGsmatrixDEG Differentially expressed genes
- MoonlightR::DiseaseListInformation on 101 biological processes
- MoonlightR::EAGenesInformation about genes
- MoonlightR::GDCprojectsInformation on GDC projects
- MoonlightR::GEO_TCGAtabInformation on GEO data (and overlap with TCGA)#' A data set containing the following data:
- MoonlightR::dataFiltGene Expression (Rnaseqv2) data from TCGA LUAD
- MoonlightR::dataGRNGRN gene regulatory network output
- MoonlightR::dataURAOutput example from function Upstram Regulator Analysis
- MoonlightR::geneInfoInformation about genes for normalization
- MoonlightR::knownDriverGenesInformation on known cancer driver gene from COSMIC
- MoonlightR::listMoonlightOutput list from Moonlight
- MoonlightR::tabGrowBlockInformation growing/blocking characteristics for 101 selected biological processes
- mosbi::mouse_dataMouse brain lipidomics data
- mosdef::res_enrich_macrophage_cluProA sample enrichment object
- mosdef::res_enrich_macrophage_goseqA sample enrichment object
- mosdef::res_enrich_macrophage_topGOA sample enrichment object
- mosdef::res_macrophage_IFNg_vs_naiveA sample 'DESeqResults' object
- MOSim::TF_humanData to extract human TF
- MOSim::associationListData to showcase scRNA and scATAC-seq association
- MOSim::sampleDataDefault data
- MOSim::scatacData to test scMOSim
- MOSim::scrnaData to test scMOSim
- motifbreakR::encodemotifMotifDb object containing motif information from the known and discovered motifs for the ENCODE TF ChIP-seq datasets.
- motifbreakR::example.pvalue
- motifbreakR::example.resultsExample Results from motifbreakR
- motifbreakR::factorbookMotifDb object containing motif information from around the genomic regions bound by 119 human transcription factors in Factorbook.
- motifbreakR::hocomocoMotifDb object containing motif information from Homo Sapiens Comprehensive Model Collection (HOCOMOCO) of transcription factor (TF) binding models
- motifbreakR::homerMotifDb object containing motif information from motif databases included in HOMER.
- motifbreakR::motifbreakR_motifMotifDb object containing motif information from the motif databases of HOCOMOCO, Homer, FactorBook and ENCODE
- motifmatchr::example_motifsexample_motifs
- motifTestR::ar_er_peaksA set of peaks with AR and ER detected
- motifTestR::ar_er_seqSequences from peaks with AR and ER detected
- motifTestR::ex_pwmExample Position Weight Matrices
- motifTestR::hg19_maskRegions from hg19 with high N content
- motifTestR::zr75_enhCandidate Enhancer Regions from ZR-75-1 Cells
- MPFE::patternsExamplepatternsExample
- mpra::mpraSetAggExampleExample data for the mpra package.
- mpra::mpraSetAllelicExampleExample data for the mpra package.
- mpra::mpraSetExampleExample data for the mpra package.
- MPRAnalyze::ce.colAnnotSample MPRA data
- MPRAnalyze::ce.controlSample MPRA data
- MPRAnalyze::ce.dnaCountsSample MPRA data
- MPRAnalyze::ce.rnaCountsSample MPRA data
- MSA2dist::AAMatrixAAMatrix-data
- MSA2dist::hivhiv-data
- MSA2dist::iupaciupac-data
- MsFeatures::seQuantified LC-MS preprocessing result test data
- msgbsR::cutsA GRanges object of differentially methylated MspI cut sites on chromosome 20 in Rat from a MS-GBS experiment.
- msgbsR::ratdataRead counts of potential MspI cut sites from a MS-GBS experiment of prostates from rats
- msgbsR::ratdata2Read counts of correct MspI cut sites from a MS-GBS experiment of prostates from rats
- msImpute::pxd007959Processed peptide intensity matrix and experimental design table from PXD007959 study
- msImpute::pxd010943SWATH-MS Analysis of Gfi1-mutant bone marrow neutrophils
- msImpute::pxd014777Processed peptide intensity matrix from PXD014777 study
- mslp::example_compSLPSLPs predicted by comp_slp
- mslp::example_comp_mutPatients mutations to be use in the comp_slp
- mslp::example_corrSLPSLPs predicted by corr_slp
- mslp::example_corr_mutPatients mutations to be use in the corr_slp
- mslp::example_exprExpression data to be used in comp_slp
- mslp::example_zExpression data to be used in corr_slp
- msmsEDA::msms.datasetLC-MS/MS dataset
- msmsEDA::pnmsAccessions and gene symbols
- msmsTests::msms.spkYeast lisate samples spiked with human proteins
- MSnbase::TMT10TMT 6/10-plex sets
- MSnbase::TMT10ETDTMT 6/10-plex sets
- MSnbase::TMT10HCDTMT 6/10-plex sets
- MSnbase::TMT11TMT 6/10-plex sets
- MSnbase::TMT11HCDTMT 6/10-plex sets
- MSnbase::TMT16TMT 6/10-plex sets
- MSnbase::TMT16HCDTMT 6/10-plex sets
- MSnbase::TMT6TMT 6/10-plex sets
- MSnbase::TMT6bTMT 6/10-plex sets
- MSnbase::TMT7TMT 6/10-plex sets
- MSnbase::TMT7bTMT 6/10-plex sets
- MSnbase::iTRAQ4iTRAQ 4-plex set
- MSnbase::iTRAQ5iTRAQ 4-plex set
- MSnbase::iTRAQ8iTRAQ 4-plex set
- MSnbase::iTRAQ9iTRAQ 4-plex set
- MSnbase::itraqdataExample 'MSnExp' and 'MSnSet' data sets
- MSnbase::msnsetExample 'MSnExp' and 'MSnSet' data sets
- MSnbase::msnset2Example 'MSnExp' and 'MSnSet' data sets
- MSnbase::nasetQuantitative proteomics data imputation
- MSnID::msnidObjExample mzIdenML File and MSnID Object
- MSPrep::COPD_131Example mass spectrometry dataset
- MSPrep::msquantExample mass spectrometry dataset.
- msqrob2::peExample data for 100 proteins
- MsQuality::metaExample data for 'MsQuality': data set of Lee et al. (2019)
- MsQuality::msexp_hilicExample data for 'MsQuality': data set of Lee et al. (2019)
- MsQuality::msexp_rplcExample data for 'MsQuality': data set of Lee et al. (2019)
- MsQuality::sps_hilicExample data for 'MsQuality': data set of Lee et al. (2019)
- MsQuality::sps_rplcExample data for 'MsQuality': data set of Lee et al. (2019)
- MsQuality::valsExample data for 'MsQuality': data set of Lee et al. (2019)
- MSstats::DDARawDataExample dataset from a label-free DDA, a controlled spike-in experiment.
- MSstats::DDARawData.SkylineExample dataset from a label-free DDA, a controlled spike-in experiment, processed by Skyline.
- MSstats::DIARawDataExample dataset from a label-free DIA, a group comparison study of S.Pyogenes.
- MSstats::SRMRawDataExample dataset from a SRM experiment with stable isotope labeled reference of a time course yeast study
- MSstats::example_SDRF
- MSstatsLiP::LiPRawDataLiPRawData
- MSstatsLiP::MSstatsLiP_SummarizedMSstatsLiP_Summarized
- MSstatsLiP::MSstatsLiP_dataMSstatsLiP_data
- MSstatsLiP::MSstatsLiP_modelMSstatsLiP_model
- MSstatsLiP::SkylineTestSkylineTest
- MSstatsLiP::TrPRawDataTrPRawData
- MSstatsLiP::raw_lipraw_lip
- MSstatsLiP::raw_protraw_prot
- MSstatsLOBD::raw_dataExample of dataset that contains spike in data for 43 distinct peptides.
- MSstatsLOBD::spikeindataExample of normalized datasets from raw_data,
- MSstatsPTM::fragpipe_annotationExample annotation file for a TMT FragPipe experiment.
- MSstatsPTM::fragpipe_annotation_proteinExample annotation file for a global profiling run TMT FragPipe experiment.
- MSstatsPTM::fragpipe_inputOutput of FragPipe TMT PTM experiment
- MSstatsPTM::fragpipe_input_proteinOutput of FragPipe TMT global profiling experiment
- MSstatsPTM::maxq_lf_annotationExample annotation file for a label-free MaxQuant experiment.
- MSstatsPTM::maxq_lf_evidenceExample MaxQuant evidence file from the output of a label free experiment
- MSstatsPTM::maxq_tmt_annotationExample annotation file for a TMT MaxQuant experiment.
- MSstatsPTM::maxq_tmt_evidenceExample MaxQuant evidence file from the output of a TMT experiment
- MSstatsPTM::pd_annotationExample annotation file for a label-free Proteome Discoverer experiment.
- MSstatsPTM::pd_psm_inputExample Proteome Discoverer evidence file from the output of a label free experiment
- MSstatsPTM::pd_testing_outputExample output of Proteome Discoverer converter
- MSstatsPTM::raw.inputExample of input PTM dataset for LabelFree/DDA/DIA experiments.
- MSstatsPTM::raw.input.tmtExample of input PTM dataset for TMT experiments.
- MSstatsPTM::spectronaut_annotationExample annotation file for a label-free Spectronaut experiment.
- MSstatsPTM::spectronaut_inputExample Spectronaut evidence file from the output of a label free experiment
- MSstatsPTM::summary.dataExample of output from dataSummarizationPTM function for non-TMT data
- MSstatsPTM::summary.data.tmtExample of output from dataSummarizationPTM_TMT function for TMT data
- MSstatsQC::QCloudDDADDA QC data from QCloud System
- MSstatsQC::QCloudSRMSRM QC data from QCloud System
- MSstatsQC::QuiCDIADIA iRT data from QuiC System
- MSstatsQC::S9Site54CPTAC study 9.1 site 54 dataset
- MSstatsQCgui::S9Site54CPTAC study 9.1 site 54 dataset
- MSstatsShiny::annotation.mineExample annotation file for Spectromine
- MSstatsShiny::annotation.mqExample annotation file for MaxQuant
- MSstatsShiny::annotation.pdExample annotation file for PD
- MSstatsShiny::dia_skyline_modelExample of Sklyine DDA dataset modeled using MSstats 'groupComparison' function.
- MSstatsShiny::dia_skyline_summarizedExample of Sklyine DDA dataset processed using MSstats summarization function.
- MSstatsShiny::evidenceExample evidence file for MaxQuant
- MSstatsShiny::example_dia_skylineExample of input Sklyine DDA dataset.
- MSstatsShiny::example_skyline_annotationExample annotation file
- MSstatsShiny::proteinGroupsExample ProteinGroups file for MaxQuant
- MSstatsShiny::raw.mineExample output file Spectromine
- MSstatsShiny::raw.omExample output file Spectromine
- MSstatsShiny::raw.pdExample output file PD
- MSstatsShiny::tmt_pd_modelExample of TMT dataset modeled using MSstatsTMT 'groupComparisonTMT' function.
- MSstatsShiny::tmt_pd_summarizedExample of TMT dataset processed using MSstatsTMT summarization function.
- MSstatsTMT::annotation.mineExample of annotation file for raw.mine, which is the output of SpectroMine.
- MSstatsTMT::annotation.mqExample of annotation file for evidence, which is the output of MaxQuant.
- MSstatsTMT::annotation.pdExample of annotation file for raw.pd, which is the PSM output of Proteome Discoverer
- MSstatsTMT::evidenceExample of output from MaxQuant for TMT-10plex experiments.
- MSstatsTMT::input.pdExample of output from PDtoMSstatsTMTFormat function
- MSstatsTMT::proteinGroupsExample of proteinGroups file from MaxQuant for TMT-10plex experiments.
- MSstatsTMT::quant.pd.msstatsExample of output from proteinSummarizaiton function
- MSstatsTMT::raw.mineExample of output from SpectroMine for TMT-6plex experiments.
- MSstatsTMT::raw.omExample of MSstatsTMT report from OpenMS for TMT-10plex experiments.
- MSstatsTMT::raw.pdExample of output from Proteome Discoverer 2.2 for TMT-10plex experiments.
- MSstatsTMT::test.pairwiseExample of output from groupComparisonTMT function
- Mulcom::AffyAffy Dataset
- Mulcom::AffyIlmncross mapping table
- Mulcom::limmaAffySymbolssignificant gene list with limma in Affymetrix
- Mulcom::limmaIlmnSymbolssignificant gene list with limma in Illumina
- Mulcom::mulcomGeneListIlmnsignificant gene list with limma in Illumina
- Mulcom::samAffySymbolssignificant gene list with SAM in Affymetrix
- Mulcom::samIlmnSymbolssignificant gene list with SAM in Illumina
- MultiAssayExperiment::miniACCAdrenocortical Carcinoma (ACC) MultiAssayExperiment
- MultiBaC::A.groTranscription rate data from yeast
- MultiBaC::A.rnaGene expression data from yeast
- MultiBaC::B.riboGene translation rate data from yeast
- MultiBaC::B.rnaGene expression data from yeast
- MultiBaC::C.parProtein binded mRNA data from yeast
- MultiBaC::C.rnaGene expression data from yeast
- MultiDataSet::rsetExample 'ResultSet'
- multiGSEA::metabolomeMetabolomic data set that is used in the toy example provided by the 'multiGSEA' package.
- multiGSEA::proteomeProteomic data set that is used in the toy example provided by the 'multiGSEA' package.
- multiGSEA::transcriptomeTranscriptomic data set that is used in the toy example provided by the 'multiGSEA' package.
- multiHiCcompare::HCT116_r1A 4 column sparse matrix for a Hi-C matrix.
- multiHiCcompare::HCT116_r2A 4 column sparse matrix for a Hi-C matrix.
- multiHiCcompare::HCT116_r3A 4 column sparse matrix for a Hi-C matrix.
- multiHiCcompare::HCT116_r4A 4 column sparse matrix for a Hi-C matrix.
- multiHiCcompare::HCT116_r5A 4 column sparse matrix for a Hi-C matrix.
- multiHiCcompare::HCT116_r6A 4 column sparse matrix for a Hi-C matrix.
- multiHiCcompare::hg19_cytoA GenomicRanges object containing centromeric, gvar, and stalk regions.
- multiHiCcompare::hg38_cytoA GenomicRanges object containing centromeric, gvar, and stalk regions.
- multiHiCcompare::hicexp2hicexp object with 4 samples from two groups.
- multiHiCcompare::hicexp_diffhicexp object with 7 samples from two groups.
- MultiMed::NavyAdenomaData from the Sinha et al. 1999 and Boca et al. 2014 studies concerning the Navy Colorectal Adenoma case-control study.
- MultimodalExperiment::pbRNAseqMultimodalExperiment Example Data
- MultimodalExperiment::scADTseqMultimodalExperiment Example Data
- MultimodalExperiment::scRNAseqMultimodalExperiment Example Data
- MultiRNAflow::RawCounts_Antoszewski2022_MOUSEsub500Mouse raw counts data
- MultiRNAflow::RawCounts_Leong2014_FISSIONsub500wtYeast times series raw counts data after stimulation with and without silencing
- MultiRNAflow::RawCounts_Schleiss2021_CLLsub500Human CCL times series raw counts data after stimulation with and without silencing
- MultiRNAflow::RawCounts_Weger2021_MOUSEsub500Mouse count data with four biological conditions, six time measurements and 500 genes.
- MultiRNAflow::Results_DEanalysis_sub500DE results of three dataset
- MultiRNAflow::Transcript_HomoSapiens_DatabaseHomo sapiens transcript database
- multiscan::murineA subset of murine macrophage gene expression data from Khondoker et al.(2006).
- multiWGCNA::permutationTestResultsPermutation test results
- multtest::golubGene expression dataset from Golub et al. (1999)
- multtest::golub.clGene expression dataset from Golub et al. (1999)
- multtest::golub.gnamesGene expression dataset from Golub et al. (1999)
- MungeSumstats::sumstatsColHeadersSummary Statistics Column Headers
- muscat::example_sceExample datasets
- muscle::umaxUnaligned MAX sequences
- musicatk::cosmic_v2_sigsCOSMIC v2 SBS96 Signatures Result Object
- musicatk::cosmic_v3_dbs_sigsCOSMIC v3 DBS Genome Signatures Result Object
- musicatk::cosmic_v3_indel_sigsCOSMIC v3 Indel Genome Signatures Result Object
- musicatk::cosmic_v3_sbs_sigsCOSMIC v3 SBS96 Genome Signatures Result Object
- musicatk::cosmic_v3_sbs_sigs_exomeCOSMIC v3 SBS96 Exome Signatures Result Object
- musicatk::dbs_musicadbs_musica
- musicatk::indel_musicaindel_musica
- musicatk::musicamusica
- musicatk::musica_annotmusica_annot
- musicatk::musica_sbs96musica_sbs96
- musicatk::musica_sbs96_tinymusica_sbs96_tiny
- musicatk::rep_rangeReplication Timing Data as GRanges Object
- musicatk::resres
- musicatk::res_annotres_annot
- MWASTools::KEGG_metabolic_pathsKEGG human metabolic pathways
- MWASTools::MS_dataSimulated LC-MS features
- MWASTools::metabo_SENMR plasma metabolic profiles dataset
- MWASTools::targetMetabo_SETarget NMR metabolites dataset
- NADfinder::single.countCounts data for chromosome 18 for an experiment of a single pair of samples
- NADfinder::triplicate.countCounts data for chromosome 18 for an expriment with triplicates
- NanoStringDiff::NanoStringDataA real 'NanoStringSet' object.
- NanoTube::ExamplePathwaysExample pathway database
- NanoTube::ExampleResultsExample results from runLimmaAnalysis
- ncGTW::xcmsExamplesExamples of xcmsSet for inputs of ncGTW
- NCIgraph::NCI.demo.cyList10 raw NCI networks from Nature curated pathways and BioCarta imported as graphNEL objects, for demonstration purpose
- netboost::tcga_aml_meth_rna_chr18TCGA RNA and methylation measurement on a subset of chromosome 18 for 80 AML patients.
- netDx::MB.phenoSample metadata table for medulloblastoma dataset.
- netDx::cnv_GRCNV locations for breast cancer (subset)
- netDx::cnv_TTstatuslist of train/test statuses for CNV example
- netDx::cnv_netPassVector of pathways that pass class enrichment
- netDx::cnv_netScoresList of pathway-level feature selection scores
- netDx::cnv_patientNetCountBinary matrix of patient occurrence in networks
- netDx::cnv_phenodata.frame of patient labels and status for CNV example
- netDx::confmatConfusion matrix example
- netDx::featScoresDemo feature-level scores from running feature selection on two-class problem
- netDx::genesTable of gene definitions (small subsample of human genes)
- netDx::modelresSample output of getResults()
- netDx::nphenoToy sample metadata table
- netDx::pathwayListSample list of pathways
- netDx::pathway_GRList of genomic ranges mapped to pathways
- netDx::phenoSample metadata table
- netDx::pheno_fullSubsample of TCGA breast cancer data used for netDx function examples
- netDx::predResExample output of getPatientRankings, used to call labels for test patients.
- netDx::silhToy network.
- netDx::toymodelExample model returned by a buildPredictor() call.
- netDx::xprExample expression matrix
- netprioR::simulationExample data: Simulated networks, phenotypes and labels for N = 1000 genes
- netresponse::dnaDna damage data set (PPI and expression)
- netresponse::osmoOsmoshock data set (PPI and expression)
- netresponse::toydatatoydata
- NetSAM::netsam_outputAn example of the list object returned by NetSAM function
- netSmooth::human.ppiHuman Protein-Protein interaction graph
- netSmooth::mouse.ppiMouse Protein-Protein interaction graph
- netSmooth::smallPPIA small human Protein-Protein interaction graph for use in examples.
- netSmooth::smallscRNAseqA small single cell RNA-seq dataset for use in examples.
- netZooR::exon.sizeGene length
- netZooR::genesExample of a gene list
- netZooR::monsterResMONSTER results from example cell-cycle yeast transition
- netZooR::mut.ucecExample of mutation data
- netZooR::small1976Pollinator-plant interactions
- netZooR::yeastToy data derived from three gene expression datasets and a mapping from transcription factors to genes.
- NeuCA::Baron_countsSingle-cell RNA-seq example dataset: Baron data
- NeuCA::Baron_true_cell_labelSingle-cell RNA-seq example dataset: Baron data
- NeuCA::Seg_countsSingle-cell RNA-seq example dataset: Seg data
- NeuCA::Seg_true_cell_labelSingle-cell RNA-seq example dataset: Seg data
- ngsReports::gcTheoreticalTheoretical GC content
- nipalsMCIA::data_blocksNCI-60 Multi-Omics Data
- nipalsMCIA::metadata_NCI60NCI-60 Multi-Omics Metadata
- NOISeq::mybiotypesMarioni's dataset
- NOISeq::mychromsMarioni's dataset
- NOISeq::mycountsMarioni's dataset
- NOISeq::mydataExample of objects used and created by the NOISeq package
- NOISeq::myfactorsMarioni's dataset
- NOISeq::mygcMarioni's dataset
- NOISeq::mylengthMarioni's dataset
- NOISeq::mynoiseqExample of objects used and created by the NOISeq package
- nondetects::nature2008The qPCR data from McMurray _et al._ Nature 2008.
- nondetects::oncogene2013The qPCR data from Sampson _et al._ Oncogene 2013.
- nondetects::sagmb2011The qPCR data from Almudevar _et al._ SAGMB 2011.
- NoRCE::brain_disorder_ncRNADifferentially expressed non-coding gene
- NoRCE::brain_mirnaDifferentially expressed human brain data
- NoRCE::breastmRNAProtein coding genes that are differentially expressed in TCGA breast cancer RNAseq data.
- NoRCE::mirnaBrain miRNA expression retrieved from the TCGA
- NoRCE::mrnaBrain mRNA expression retrieved from the TCGA
- NoRCE::ncRegionDifferentially expressed non-coding gene regions
- NoRCE::tad_dmelTAD regions for the fly
- NoRCE::tad_hg19TAD regions for human hg19 assembly
- NoRCE::tad_hg38TAD regions for human hg38 assembly
- NoRCE::tad_mm10TAD regions for mouse
- NormalyzerDE::example_dataSmall example dataset used to demonstrate code consistency in testing and as dummy data in the vignette.
- NormalyzerDE::example_dataSmall example dataset used to demonstrate code consistency in testing and as dummy data in the vignette.
- NormalyzerDE::example_data_only_valuesSame data as in "example_data", but omitting the annotation meaning that it only contains the expression data.
- NormalyzerDE::example_data_only_valuesSame data as in "example_data", but omitting the annotation meaning that it only contains the expression data.
- NormalyzerDE::example_designDesign matrix corresponding to the small example datasets.
- NormalyzerDE::example_designDesign matrix corresponding to the small example datasets.
- NormalyzerDE::example_stat_dataSame data as in "example_data", but normalized and ready for statistical processing.
- NormalyzerDE::example_stat_summarized_experimentSummarizedExperiment object prepared with design-matrix, data-matrix and annotation columns for normalized data
- NormalyzerDE::example_summarized_experimentSummarizedExperiment object prepared with design-matrix, data-matrix and annotation columns loaded for raw data
- NormalyzerDE::example_wide_dataFull raw NormalyzerDE matrix used for internal testing
- NormalyzerDE::example_wide_designDesign matrix belonging together with example_wide_data. Used for internal testing.
- NormqPCR::BladderBladder dataset of Andersen et al (2004)
- NormqPCR::BladderReproDataset of Andersen et al (2004)
- NormqPCR::ColonColon dataset of Andersen et al (2004)
- NormqPCR::geNorm.qPCRBatchData set of Vandesompele et al (2002)
- NPARC::stauro_TPP_data_tidyTPP dataset of staurosporine treated cells.
- NTW::sos.dataSOS pathway perturbation data
- nucleR::nucleosome_htseqExample reads from high-troughtput sequencing nucleosome positioning experiment
- nucleR::nucleosome_tilingExample intensities from Tiling Microarray nucleosome positioning experiment
- occugene::sampleAnnotationAnnotation for a Hypothetical Prokayote
- occugene::sampleInsertionsInsertions for a Hypothetical Clonal Library
- octad::res_exampleDifferential expression example for HCC vs adjacent liver tissue computed in diffExp() function
- octad::sRGES_exampleData of computed example sRGEs for HCC vs liver adjacent tissues on octad.small dataset
- odseq::seqsPFAM plus random data.
- oligoClasses::efsExampleExpressionFeatureSet Object
- oligoClasses::locusLevelDataBasic data elements required for the HMM
- oligoClasses::oligoSetAn example instance of oligoSnpSet class
- oligoClasses::scqsExampleSnpCnvQSet Example
- oligoClasses::sfsExampleSnpFeatureSet Example
- oligoClasses::sqsExampleSnpQSet Example
- OLIN::swcDNA microarray data of SW480/SW620 experiment
- OLIN::sw.olinNormalised cDNA microarray data of SW480/SW620 experiment
- OLIN::sw.xySpatial coordinates of spot locations of SW480/SW620 experiment
- omada::toy_gene_membershipsCluster memberships for toy gene data for package examples
- omada::toy_genesToy gene data for package examples
- OmaDB::groupAn example OMA group object.
- OmaDB::hogAn example HOG object.
- OmaDB::orthologsAn example orthologs object.
- OmaDB::pairsAn example genome alignment object.
- OmaDB::proteinAn example protein object.
- OmaDB::sequence_annotationAn example dataframe containing GO annotations identified from a given sequence.
- OmaDB::sequence_mapAn example dataframe containing proteins identified from a given sequence.
- OmaDB::taxonomyAn example newick format taxonomy object.
- OmaDB::xrefAn example xref object.
- omicade4::NCI60_4arraysMicroarray gene expression profiles of the NCI 60 cell lines from 4 different platforms
- OmicCircos::TCGA.BC.cnv.2k.60copy number data of TCGA Breast Cancer
- OmicCircos::TCGA.BC.fusTCGA Breast Cancer gene fusion data.
- OmicCircos::TCGA.BC.gene.exp.2k.60TCGA BRCA expression data
- OmicCircos::TCGA.BC.sample60TCGA BRCA Sample names and subtypes
- OmicCircos::TCGA.BC_Her2_cnv_expTCGA BRCA expression and cnv association
- OmicCircos::TCGA.PAM50_genefu_hg18BRCA PAM50 gene list (hg18)
- OmicCircos::UCSC.chr.colorschromosome banding colors
- OmicCircos::UCSC.hg18human hg18 circumference coordinates
- OmicCircos::UCSC.hg18.chrhuman hg18 segment data.
- OmicCircos::UCSC.hg19human hg19 circumference coordinates
- OmicCircos::UCSC.hg19.chrhuman hg19 segment data
- OmicCircos::UCSC.mm10mouse mm10 circumference coordinates
- OmicCircos::UCSC.mm10.chrmouse mm10 segment data.
- OmicCircos::UCSC.mm9mouse mm9 circumference coordinates
- OmicCircos::UCSC.mm9.chrmouse mm9 segment data.
- omicplotR::metadataVaginal microbiome OTU table metadata
- omicplotR::otu_tableVaginal microbiome OTU table
- omicRexposome::asr'ResultSet' for testing and illustration purpouses
- omicRexposome::crs'ResultSet' for testing and illustration purpouses
- omicRexposome::mds'MultiDataSet' for testing and illustration purpouses
- omicsPrint::hg19.GoNLsnpsDataframe with overlaps GoNL variants and 450K probes
- omicsPrint::hm450.manifest.pop.GoNLHM450 population-specific probe-masking recommendations
- oncomix::exprNmlIsofHuman Breast Cancer RNA-sequencing data from TCGA - Adj. Normal Tissue
- oncomix::exprTumIsofHuman Breast Cancer RNA-sequencing data from TCGA - Tumor Tissue
- oncomix::queryResOncogene Database Mapping Gene Symbol to UCSC ID (kgID)
- oncoscanR::oncoscan_na33.covGenomicRanges object of the chromosomal arms coverage for the oncoscan assay (based on file extdata/Oncoscan.na33.r2.cov.processed.bed).
- oncoscanR::segs.chas_exampleExpected segments from loading the ChAS file 'chas_example.txt'.
- OncoScore::genesA list of genes
- OncoScore::queryThe result of perform.web.query on genes
- OncoScore::query.timepointsThe result of perform.time.series.query on genes and timepoints
- OncoScore::timepointsA list of timepoints
- OncoSimulR::atex2bRuns from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
- OncoSimulR::atex4Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
- OncoSimulR::atex5Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
- OncoSimulR::benchmark_1Summary results from some benchmarks reported in the vignette.
- OncoSimulR::benchmark_1_0.05Summary results from some benchmarks reported in the vignette.
- OncoSimulR::benchmark_2Summary results from some benchmarks reported in the vignette.
- OncoSimulR::benchmark_3Summary results from some benchmarks reported in the vignette.
- OncoSimulR::ex_missing_drivers_b11An example where there are intermediate missing drivers.
- OncoSimulR::ex_missing_drivers_b12An example where there are intermediate missing drivers.
- OncoSimulR::examplePosetsExample posets
- OncoSimulR::examplesFitnessEffectsExamples of fitness effects
- OncoSimulR::mcfLsmcfLs simulation from the vignette
- OncoSimulR::osiRuns from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
- OncoSimulR::osi_with_intsRuns from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
- OncoSimulR::s_3_aRuns from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
- OncoSimulR::s_3_bRuns from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
- OncoSimulR::simT2Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
- OncoSimulR::simT3Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
- OncoSimulR::simul_period_1Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
- OncoSimulR::smyelo3v57Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
- OncoSimulR::uvex2Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
- OncoSimulR::uvex3Runs from simulations of interventions examples shown in the vignette. Most, but not all, are from intervention examples.
- OncoSimulR::woAntibSRuns from simulations of frequency-dependent examples shown in the vignette.
- ontoProc::PROSYMPROSYM: HGNC symbol synonyms for PR (protein ontology) entries identified in Cell Ontology
- ontoProc::allGOtermsallGOterms: data.frame with ids and terms
- ontoProc::humrnahumrna: a data.frame of SRA metadata related to RNA-seq in humans
- ontoProc::minicorpusminicorpus: a vector of annotation strings found in 'study title' of SRA metadata.
- ontoProc::packDesc2019packDesc2019: overview of ontoProc resources
- ontoProc::packDesc2021packDesc2021: overview of ontoProc resources
- ontoProc::packDesc2022packDesc2022: overview of ontoProc resources
- ontoProc::packDesc2023packDesc2023: overview of ontoProc resources
- ontoProc::stopWordsstopWords: vector of stop words from xpo6.com
- openPrimeR::feature.matrixData Sets.
- openPrimeR::primer.dataData Sets.
- openPrimeR::primer.dataData Sets.
- openPrimeR::primer.dfData Sets.
- openPrimeR::ref.dataData Sets.
- openPrimeR::settingsData Sets.
- openPrimeR::settingsData Sets.
- openPrimeR::template.dataData Sets.
- openPrimeR::template.dfData Sets.
- openPrimeR::tiller.primer.dfData Sets.
- openPrimeR::tiller.settingsData Sets.
- openPrimeR::tiller.template.dfData Sets.
- oposSOM::hsa03320.RData
- oposSOM::hsa04010.RData
- oposSOM::hsa04012.RData
- oposSOM::hsa04014.RData
- oposSOM::hsa04015.RData
- oposSOM::hsa04020.RData
- oposSOM::hsa04022.RData
- oposSOM::hsa04024.RData
- oposSOM::hsa04062.RData
- oposSOM::hsa04064.RData
- oposSOM::hsa04066.RData
- oposSOM::hsa04068.RData
- oposSOM::hsa04070.RData
- oposSOM::hsa04071.RData
- oposSOM::hsa04072.RData
- oposSOM::hsa04115.RData
- oposSOM::hsa04150.RData
- oposSOM::hsa04151.RData
- oposSOM::hsa04152.RData
- oposSOM::hsa04261.RData
- oposSOM::hsa04310.RData
- oposSOM::hsa04330.RData
- oposSOM::hsa04340.RData
- oposSOM::hsa04350.RData
- oposSOM::hsa04370.RData
- oposSOM::hsa04371.RData
- oposSOM::hsa04390.RData
- oposSOM::hsa04392.RData
- oposSOM::hsa04550.RData
- oposSOM::hsa04620.RData
- oposSOM::hsa04621.RData
- oposSOM::hsa04622.RData
- oposSOM::hsa04625.RData
- oposSOM::hsa04630.RData
- oposSOM::hsa04657.RData
- oposSOM::hsa04660.RData
- oposSOM::hsa04662.RData
- oposSOM::hsa04664.RData
- oposSOM::hsa04668.RData
- oposSOM::hsa04722.RData
- oposSOM::hsa04723.RData
- oposSOM::hsa04910.RData
- oposSOM::hsa04912.RData
- oposSOM::hsa04915.RData
- oposSOM::hsa04917.RData
- oposSOM::hsa04919.RData
- oposSOM::hsa04920.RData
- oposSOM::hsa04921.RData
- oposSOM::hsa04922.RData
- oposSOM::hsa04926.RData
- oposSOM::hsa04933.RData
- oposSOM::hsa05120.RData
- oposSOM::kegg.collection.RData
- oposSOM::opossom.genesetsAdditional literature genesets
- oposSOM::opossom.tissuesExample data set.
- oppar::bcmBreast cancer metastases from different anatomical sites
- oppar::esetTomlins et al. Prostate Cancer data (GEO: GSE6099)
- oppar::maupinMaupin's TGFb data and a TGFb gene signature
- OrderedList::OL.dataGene Expression and Clinical Information of Two Cancer Studies
- OrderedList::OL.resultThree Examples of Class 'OrderedList'
- orthogene::exp_mouseGene expression data: mouse
- orthogene::exp_mouse_enstTranscript expression data: mouse
- OSAT::BeadChip96ToMSA4MAPClass '"MSAroboticPlate"'
- OSAT::GenotypingChipClass '"BeadChip"'
- OSAT::IlluminaBeadChipClass '"BeadChip"'
- OSAT::IlluminaBeadChip24PlateClass '"BeadPlate"'
- OSAT::IlluminaBeadChip48PlateClass '"BeadPlate"'
- OSAT::IlluminaBeadChip96PlateClass '"BeadPlate"'
- OSAT::MSA4.plateClass '"MSAroboticPlate"'
- OSAT::gSetupR data object based on example file.
- OSAT::gSetup2R data object based on example file.
- OSAT::gcR data object based on example file.
- OSAT::gsR data object based on example file.
- OSAT::phenoR data object based on example file.
- Oscope::OscopeExampleDataSimulated gene level data set with 600 genes and 30 cells.
- OVESEG::RocheBTmRNA expression data downsampled from GSE28490 (Roche)
- OVESEG::countBTRNAseq count data downsampled from GSE60424
- packFinder::arabidopsisThalianaRefseqArabidopsis thaliana Refseq Genome Chromosome 3 Subset
- packFinder::packMatchesSample packFinder Output
- padma::LUAD_subsetSubset of batch-corrected multi-omic TCGA data in lung adenocarcinoma
- padma::mirtarbaseCurated miR-target interaction predictions from miRTarBase
- padma::msigdbMSigDB canonical pathways and corresponding gene lists
- PAIRADISE::sample_datasetsample_dataset
- PAIRADISE::sample_dataset_CEUsample_dataset
- PAIRADISE::sample_dataset_LUSCsample_dataset
- paircompviz::brokentransArtificial dataset that suffers with broken transitivity of the pairwise t-test comparisons
- pairedGSEA::example_diff_resultOutput of running paired_diff on example_se.
- pairedGSEA::example_gene_setsMSigDB gene sets from humans, category C5 with ensemble gene IDs
- pairedGSEA::example_ora_resultsOutput of running paired_ora on example_diff_result and gene sets extracted from MSigDB
- pairedGSEA::example_seA small subset of the GEO:GSE61220 data set.
- pairkat::smokersSmokers - PaIRKAT Example Data
- pandaR::pandaResultAnalysis result from PANDA algorithm on toy data
- pandaR::pandaResultPairsAnalysis result from PANDA algorithm on toy data converted into pairs
- pandaR::pandaToyDataToy gene expression, motif, and ppi data
- panelcn.mops::controlGRanges object of countWindows with read counts for control samples as elementMetadata.
- panelcn.mops::countWindowsresult object of getWindows - a data.frame with the contents of the provided BED file with an additional gene name and exon name column
- panelcn.mops::read.widthread width used for calculating RCs of test and control
- panelcn.mops::resultlistresult object of runPanelcnMops - a list of instances of "CNVDetectionResult"
- panelcn.mops::testGRanges object of countWindows with read counts for a test sample as elementMetadata.
- PanomiR::gscExampleExample genesets from MSigDB
- PanomiR::miniTestsPanomiRReadouts and datasets for minimal reproducible examples of the PanomiR.
- PanomiR::msigdb_c2Canonical pathways from Molecular Signatures Database, MsigDb V6.2
- PanomiR::path_gene_tableA table of gene-pathway association. based on the pathways of MSigDB.
- PanomiR::targetScan_03A processed list of miRNA target gene sets from the TargetScan dataset. Each list item is a list of genes targeted by the respective miRNA family
- panp::NSMPnames.hgu133aNegative Strand Matching Probeset (NSMP) names for HG-U133A chip type
- panp::NSMPnames.hgu133plus2Negative Strand Matching Probeset (NSMP) names for HG-U133 Plus 2.0 chip type
- panp::gcrma.ExpressionSetExpressionSet resulting from gcrma processing of 3 HG-U133A chips
- PANR::Bakal2007Rich morphological phenotypes for gene overexpression and RNA interference screens
- PANR::Bakal2007ClusterRich morphological phenotypes for gene overexpression and RNA interference screens
- PANR::bm1Rich morphological phenotypes for gene overexpression and RNA interference screens
- PANR::nodeColorRich morphological phenotypes for gene overexpression and RNA interference screens
- PanViz::er_snp_vectorSummary-level GWAS data vector for estrogen-receptor positive breast cancer (EFO_1000649)
- pareg::pathway_similaritiesCollection of pathway similarity matrices.
- parody::bushfiresatellite data on bushfire scars
- parody::tcostData on milk transportation costs, from Johnson and Wichern, Applied Multivariate Statistical Analysis, 3rd edition
- partCNV::Hg38_gtfGTF data for Hg38 genome
- partCNV::SimDataSimulation data to examplify the usage of the method
- partCNV::SimDataSceSimulation SingleCellExperiment object to examplify the usage of the method
- Path2PPI::human.ai.irefindexData set to predict autophagy induction in _Podospora anserina_
- Path2PPI::human.ai.proteinsData set to predict autophagy induction in _Podospora anserina_
- Path2PPI::pa2human.ai.homologsData set to predict autophagy induction in _Podospora anserina_
- Path2PPI::pa2yeast.ai.homologsData set to predict autophagy induction in _Podospora anserina_
- Path2PPI::yeast.ai.irefindexData set to predict autophagy induction in _Podospora anserina_
- Path2PPI::yeast.ai.proteinsData set to predict autophagy induction in _Podospora anserina_
- pathifier::KEGGTwo pathways of the KEGG database
- pathifier::ShefferSheffer et al. colorectal dataset
- pathlinkR::exampleDESeqResultsList of example results from DESeq2
- pathlinkR::groupedPathwayColoursColour assignments for grouped pathways
- pathlinkR::hallmarkDatabaseTable of Hallmark gene sets and their genes
- pathlinkR::innateDbPPIInnateDB PPI data
- pathlinkR::keggDatabaseTable of KEGG pathways and genes
- pathlinkR::mappingFileTable of human gene ID mappings
- pathlinkR::pathwayCategoriesTop-level pathway categories
- pathlinkR::reactomeDatabaseTable of all Reactome pathways and genes
- pathlinkR::sigoraDatabaseTable of all Sigora pathways and their constituent genes
- pathlinkR::sigoraExamplesSigora enrichment example
- PathoStat::pstatpathostat object generated from example pathoscope report files
- PathoStat::pstatpathostat object generated from example pathoscope report files
- PathoStat::pstatpathostat object generated from example pathoscope report files
- PathoStat::pstatpathostat object generated from example pathoscope report files
- pathview::KEGGEdgeSubtypeInternal functions
- pathview::bodsMapping data on KEGG species code and corresponding Bioconductor gene annotation package
- pathview::cpd.accsMapping data between compound or gene IDs and KEGG accessions
- pathview::cpd.namesMapping data between compound or gene IDs and KEGG accessions
- pathview::cpd.simtypesMapping data between compound or gene IDs and KEGG accessions
- pathview::demo.pathsData for demo purpose
- pathview::gene.idtype.bodsMapping data between compound or gene IDs and KEGG accessions
- pathview::gene.idtype.listMapping data between compound or gene IDs and KEGG accessions
- pathview::gse16873.dData for demo purpose
- pathview::kegg.metMapping data between compound or gene IDs and KEGG accessions
- pathview::ko.idsMapping data between compound or gene IDs and KEGG accessions
- pathview::korgMapping data on KEGG species code and corresponding Bioconductor gene annotation package
- pathview::paths.hsaData for demo purpose
- pathview::rn.listMapping data between compound or gene IDs and KEGG accessions
- pathwayPCA::colonSurv_dfColon Cancer -Omics Data
- pathwayPCA::colon_pathwayCollectionGene Pathway Subset
- pathwayPCA::wikipwsHS_Entrez_pathwayCollectionWikipathways Homosapiens EntrezIDs
- pathwayPCA::wikipwsHS_Symbol_pathwayCollectionWikipathways Homosapiens Gene Symbols
- pcaMethods::helixA helix structured toy data set
- pcaMethods::metaboliteDataA incomplete metabolite data set from an Arabidopsis coldstress experiment
- pcaMethods::metaboliteDataCompleteA complete metabolite data set from an Arabidopsis coldstress experiment
- PCAN::geneByHpEntrez gene IDs associated to HP terms (Example data)
- PCAN::geneByTraitGene associated to trait (Example data)
- PCAN::geneDefDescription of genes (Example data)
- PCAN::hpByTraitHP IDs associated to trait (Example data)
- PCAN::hpDefDescription of HP terms (Example data)
- PCAN::hp_ancestorsHP ancestors (Example data)
- PCAN::hp_classHP class (Example data)
- PCAN::hp_descendantsHP descendants (Example data)
- PCAN::hqStrNwSTRIND database network of Homo sapiens genes (Example data)
- PCAN::hsEntrezByRPathHomo sapiens entrez gene ID by Reactome pathway (Example data)
- PCAN::rPathReactome pathways (Example data)
- PCAN::traitDefDescription of Traits (Example data)
- PDATK::CSPC_MAEA 'MultiAssayExperiment' containing cohorts of pancreatic cancer patients, for use in package examples.
- PDATK::birnbaumPublished classifier gene signature for Birnbaum
- PDATK::chenPublished classifier gene signature for Chen
- PDATK::cohortSubtypeDFsA list of sample subtypes for the data in sampleCohortList
- PDATK::haiderSigScoresClassifier survival scores for Haider
- PDATK::sampleClinicalModelSample ClinicalModel Containing the ICGC micro-array cohort from 'MetaGxPancreas' as training data.
- PDATK::sampleCohortListA Set of Example Patient Cohorts
- PDATK::sampleICGCmicroA Sample SurvivalExperiment Containing Data from the ICGC micro-array cohort from 'MetaGxPancreas'
- PDATK::samplePCOSPmodelA Sample PCOSP Model Containing the ICGC micro-array cohort from 'MetaGxPancreas' as training data.
- PDATK::samplePCOSPpredListSample CohortList with PCOSP Risk Predictions
- PDATK::samplePCSIsurvExpSample SurvivalExperiment Containing the PCSI rna-sequencing cohort from 'MetaGxPancreas'.
- PDATK::sampleRGAmodelSample RGA Model Containing the ICGC micro-array cohort from 'MetaGxPancreas' as training data.
- PDATK::sampleRLSmodelSample RLS Model Containing the ICGC micro-array cohort from 'MetaGxPancreas' as training data.
- PDATK::sampleTrainedPCOSPmodelA Sample Trained PCOSP Model Containing the ICGC micro-array cohort from 'MetaGxPancreas' as training data.
- PDATK::sampleValPCOSPmodelSample Validated PCOSP Model for Plotting Examples
- peco::cellcyclegenes_whitfield2002list of cell cycle genes identified in Whitfield et al. 2002.
- peco::model_5genes_predictA SingleCellExperiment object
- peco::model_5genes_trainTraing model results among samples from 5 individuals.
- peco::sce_top101genesMolecule counts of the 101 significant cyclical genes in the 888 samples analyzed in the study.
- peco::training_humanTraining data from 888 single-cell samples and 101 top cyclic genes
- Pedixplorer::minnbreastMinnesota Breast Cancer Study
- Pedixplorer::samplepedSampleped data
- periodicDNA::ce11_ATACseqce11_ATACseq
- periodicDNA::ce11_TSSsce11_TSSs
- periodicDNA::ce11_WW_10bpce11_WW_10bp
- periodicDNA::ce11_all_REsce11_all_REs
- periodicDNA::ce11_promsce11_proms
- periodicDNA::ce11_proms_seqsce11_proms_seqs
- pgca::BET1947_v339Data Files From BiT Heart Cohort
- pgca::BET2007_v339Data Files From BiT Heart Cohort
- pgca::BET2047_v339Data Files From BiT Heart Cohort
- pgca::BET2067_v339Data Files From BiT Heart Cohort
- pgxRpi::hg19_cytobandA dataframe containing cytoband annotation details extracted from the hg19 gennome. It is used for CNV frequency visualization.
- pgxRpi::hg38_cytobandA dataframe containing cytoband annotation details extracted from the hg38 gennome. It is used for CNV frequency visualization.
- phantasus::esExample dataset
- phantasus::fgseaExampleExample pathway data.frame for fgsea tool
- PharmacoGx::CCLEsmallCancer Cell Line Encyclopedia (CCLE) Example PharmacoSet
- PharmacoGx::CMAPsmallConnectivity Map Example PharmacoSet
- PharmacoGx::GDSCsmallGenomics of Drug Sensitivity in Cancer Example PharmacoSet
- PharmacoGx::HDAC_genesHDAC Gene Signature
- phenoTest::ephenoepheno object.
- phenoTest::esetExample data.
- phenoTest::eset.genelevelExample data.
- phosphonormalizer::enriched.rdEnriched dataset
- phosphonormalizer::non.enriched.rdNon-enriched dataset
- PhosR::KinaseFamilyKinaseFamily
- PhosR::PhosphoSite.humanPhosphoSitePlus annotations for human
- PhosR::PhosphoSite.mousePhosphoSitePlus annotations for mouse
- PhosR::PhosphoSite.ratPhosphoSitePlus annotations for rat
- PhosR::SPSsA list of Stably Phosphorylated Sites (SPSs)
- PhosR::hSEGsA list of Stably Expressed Genes (SEGs)
- PhosR::mSEGsA list of Stably Expressed Genes (SEGs)
- PhosR::motif.human.listList of human kinase motifs
- PhosR::motif.mouse.listList of mouse kinase motifs
- PhosR::motif.rat.listList of rat kinase motifs
- PhosR::phospho.L6.ratiophospho.L6.ratio
- PhosR::phospho.L6.ratio.pephospho_L6_ratio_pe
- PhosR::phospho.cells.Insphospho.cells.Ins
- PhosR::phospho.cells.Ins.pephospho.cells.Ins
- PhosR::phospho.liver.Ins.TC.ratio.RUVphospho_liverInsTC_RUV_sample
- PhosR::phospho.liver.Ins.TC.ratio.RUV.pephospho.liver.Ins.TC.ratio.RUV.pe
- PhyloProfile::filteredProfileAn example of a filtered phylogenetic profile
- PhyloProfile::finalProcessedProfileAn example of a final processed & filtered phylogenetic profile
- PhyloProfile::fullProcessedProfileAn example of a fully processed phylogenetic profile
- PhyloProfile::idListNCBI ID list for experimental data sets
- PhyloProfile::mainLongRawAn example of a raw long input file
- PhyloProfile::ppTaxonomyMatrixAn example of a taxonomy matrix
- PhyloProfile::ppTreeAn example of a taxonomy tree in newick format
- PhyloProfile::profileWithTaxonomyAn example of a raw long input file together with the taxonomy info
- PhyloProfile::rankListNCBI rank list for experimental data sets
- PhyloProfile::taxonNamesReducedNCBI Taxonomy reduced data set
- PhyloProfile::taxonomyMatrixTaxonomy matrix for experimental data sets
- phyloseq::GlobalPatterns(Data) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample (2011)
- phyloseq::enterotype(Data) Enterotypes of the human gut microbiome (2011)
- phyloseq::esophagus(Data) Small example dataset from a human esophageal community (2004)
- phyloseq::soilrep(Data) Reproducibility of soil microbiome data (2011)
- piano::gsa_inputRandom input data for gene set analysis
- piano::gsa_resultsGene set analysis result data
- Pigengene::amlAML gene expression profile
- Pigengene::eigengenes33Eigengenes of 33 modules
- Pigengene::mdsMDS gene expression profile
- Pigengene::pigengeneAn object of class 'Pigengene'
- pipeComp::clustMetricsCorrCorrelations across clustering evaluation metrics
- pipeComp::ctrlgenesLists of control genes
- pipeComp::exampleDEAresultsExample results from the DEA pipeline
- pipeComp::exampleResultsExample pipeline results
- pipeComp::stableGLists of stable genes
- Pirat::ropersRopers dataset
- Pirat::subbouyssieSub-Bouyssie dataset
- Pirat::subropersSub-Ropers dataset
- PIUMA::df_test_projA dataset to test the 'dfToProjection' and 'dfToDistance' funtions of 'PIUMA' package.
- PIUMA::tda_test_dataA TDAobj to test the 'PIUMA' package.
- PIUMA::vascEC_metaExample datasets for PIUMA package
- PIUMA::vascEC_normWe tested PIUMA on a subset of the single-cell RNA Sequencing dataset (GSE:GSE193346 generated and published by Feng et al. (2022) on Nature Communication to demonstrate that distinct transcriptional profiles are present in specific cell types of each heart chambers, which were attributed to have roles in cardiac development. In this tutorial, our aim will be to exploit PIUMA for identifying sub-population of vascular endothelial cells, which can be associated with specific heart developmental stages. The original dataset consisted of three layers of heterogeneity: cell type, stage and zone (i.e., heart chamber). Our testing dataset was obtained by subsetting vascular endothelial cells (cell type) by Seurat object, extracting raw counts and metadata. Thus, we filtered low expressed genes and normalized data by DaMiRseq
- planet::ageCpGsPlacental gestational age CpGs
- planet::ethnicityCpGsCpGs to predict ethnicity
- planet::plBetasExample placental DNA methylation data
- planet::plCellCpGsFirstFirst trimester placental cell type coefficients
- planet::plCellCpGsThirdThird trimester placental cell type coefficients
- planet::plColorsA color palette for placental cell types
- planet::plPhenoDataSample information accompanying 'pl_betas'
- planttfhunter::classification_schemeData frame of TF family classification scheme
- planttfhunter::gsuProtein sequences of the algae species Galdieria sulphuraria
- planttfhunter::gsu_annotationDomain annotation for the algae species Galdieria sulphuraria The data set was created using the funcion 'annotate_pfam()' in local mode.
- planttfhunter::gsu_familiesTFs families of the algae species Galdieria sulphuraria The data set was created using the funcion 'classify_tfs()'.
- planttfhunter::tf_countsTF counts per family in 4 simulated species
- plasmut::crcseqThis data is an example dataset to show how to use the package
- plgem::LPSesetExpressionSet for Testing PLGEM
- PLPE::plateletSetLCMS proteomic data for platelte MPs
- PLSDAbatch::AD_dataAnaerobic digestion study
- PLSDAbatch::sponge_dataSponge _A. aerophoba_ study
- plyinteractions::GM12878_HiCCUPSLoops identified in GM12878 with HiCCUPS
- plyinteractions::ce10_ARCCInteractions identified in L3 C. elegans by ARC-C
- plyinteractions::ce10_REsAnnotated regulatory elements in C. elegans
- pmm::kinomeExample Data from InfectX
- pmp::MTBLS79Direct-infusion mass spectrometry (DIMS) data set
- PoDCall::thrTablePoDCall Example Threshold Table
- podkat::b36UnmaskedUnmasked Regions of Human Genomes
- podkat::b37UnmaskedUnmasked Regions of Human Genomes
- podkat::hg18UnmaskedUnmasked Regions of Human Genomes
- podkat::hg19UnmaskedUnmasked Regions of Human Genomes
- podkat::hg38UnmaskedUnmasked Regions of Human Genomes
- podkat::hgAArtificial Human Chromosome for Testing Purposes
- pogos::CCLE_drtscompounds_v1: serialization of compounds info from PharmacoDb v1
- pogos::cell_lines_v1compounds_v1: serialization of compounds info from PharmacoDb v1
- pogos::compounds_v1compounds_v1: serialization of compounds info from PharmacoDb v1
- pogos::datasets_v1compounds_v1: serialization of compounds info from PharmacoDb v1
- pogos::tissues_v1compounds_v1: serialization of compounds info from PharmacoDb v1
- PolySTest::liver_exampleExample data set liver_example for PolySTest
- POMA::st000284Colorectal Cancer Detection Using Targeted Serum Metabolic Profiling
- POMA::st000336Targeted LC/MS of urine from boys with DMD and controls
- powerTCR::repertoiresTwo toy examples of sample TCR repertoires.
- POWSC::es_mef_scesample data for POWSC
- POWSC::scesample data for GSE67835
- ppcseq::countscounts
- preciseTAD::arrowhead_gm12878_5kbDomain data from ARROWHEAD TAD-caller for GM12878 at 5 kb
- preciseTAD::tfbsListA list of the chromosomal coordinates for 26 transcription factor binding sites from the Gm12878 cell line
- PrInCE::gold_standardReference set of human protein complexes
- PrInCE::kristensenInteractome of HeLa cells
- PrInCE::kristensen_gaussiansFitted Gaussian mixture models for the 'kristensen' dataset
- PrInCE::scottCytoplasmic interactome of Jurkat T cells during apoptosis
- PrInCE::scott_gaussiansFitted Gaussian mixture models for the 'scott' dataset
- proActiv::promoterAnnotation.gencode.v34.subsetPromoter annotation for Gencode.v34 (subset)
- procoil::PrOCoilModelClass "CCModel"
- procoil::PrOCoilModelBAClass "CCModel"
- profileplyr::K27ac_GRlist_hind_liver_top5000GRangesList of the top 5000 H3K27ac peaks from hindbrain and liver downloaded from ENCODE
- profileplyr::gene_list_characterCharacter vector of the top differentially expressed genes from hindbrain versus liver as measured by RNA-seq
- profileplyr::gene_list_dataframeDataframe of top differentially expressed genes from hindbrain versus liver as measured by RNA-seq
- profileScoreDist::INRThe position count matrix for INR.
- progeny::model_human_fullThe full human linear model underlying PROGENy
- progeny::model_mouse_fullThe full mouse linear model underlying PROGENy
- progeny::vignette_dataThe RNA data used in the progeny vignette
- projectR::AP.RNAseq6l3c3tCoGAPS patterns and genes weights for p.RNAseq6l3c3t
- projectR::CR.RNAseq6l3c3tCogapsResult object for p.RNAseq6l3c3t
- projectR::cr_microglialCogapsResult object for microglial_counts
- projectR::glial_countslog-normalized count data from astrocytes and oligodendrocytes in the p6 mouse cortex.
- projectR::map.ESepiGen4c1lRNAseqing and ChIPSeq of matched genes in differentiated human iPS cells
- projectR::map.RNAseq6l3c3tRNAseqing from human 3 iPS & 3 ES cell lines in 3 experimental condition at 3 time points
- projectR::microglial_countslog-normalized count data from microglial cells in the p6 mouse cortex.
- projectR::multivariateAnalysisR_seurat_testTruncated Seurat Object with latent space projection done to unspecified cells in different stages for multivariateAnalysisR analysis
- projectR::p.ESepiGen4c1lRNAseqing and ChIPSeq of matched genes in differentiated human iPS cells
- projectR::p.RNAseq6l3c3tRNAseqing from human 3 iPS & 3 ES cell lines in 3 experimental condition at 3 time points
- projectR::pd.ESepiGen4c1lRNAseqing and ChIPSeq of matched genes in differentiated human iPS cells
- projectR::pd.RNAseq6l3c3tRNAseqing from human 3 iPS & 3 ES cell lines in 3 experimental condition at 3 time points
- projectR::retinal_patternsCoGAPS patterns learned from the developing mouse retina.
- pRoloc::andy2011paramsClass '"AnnotationParams"'
- pRoloc::dunkley2006paramsClass '"AnnotationParams"'
- PROMISE::phPattPhenotype Pattern Definition Set
- PROMISE::sampExprSetAn Example Expression Set
- PROMISE::sampGeneSetAn Example Gene Set Collection
- PROPER::GE.humanSome existing RNA-seq and gene expression microarray data
- PROPER::paramSome existing RNA-seq and gene expression microarray data
- PROPER::paramSome existing RNA-seq and gene expression microarray data
- PROPER::paramSome existing RNA-seq and gene expression microarray data
- PROPER::paramSome existing RNA-seq and gene expression microarray data
- PROPER::pbmcSome existing RNA-seq and gene expression microarray data
- PROPS::example_dataExample data, 50 samples, 22600 genes.
- PROPS::example_edgesExample pathway edges. Contains 3 randomly generated pathways.
- PROPS::example_healthyExample healthy data, 100 samples, 22600 genes.
- PROPS::kegg_pathway_edgesKEGG pathway edges
- proteinProfiles::annotationIPS sample data
- proteinProfiles::ratiosIPS sample data
- ProteoDisco::ProteoDiscographyExample.hg19Example ProteoDiscography.
- ProteoMM::hs_peptideshs_peptides - peptide-level intensities for human
- ProteoMM::mm_peptidesmm_peptides - peptide-level intensities for mouse
- psygenet2r::qr'DataGeNET.Psy' obtained from quering PsyGeNET for gene '4852'.
- psygenet2r::universeVector with gene universe for Jaccard Index
- puma::Clust.exampleEThe example data of the mean gene expression levels
- puma::Clust.exampleStdThe example data of the standard deviation for gene expression levels
- puma::Clustii.exampleEThe example data of the mean gene expression levels
- puma::Clustii.exampleStdThe example data of the standard deviation for gene expression levels
- puma::eset_mmgmosAn example ExpressionSet created from the Dilution data with mmgmos
- puma::exampleEThe example data of the mean gene expression levels
- puma::exampleStdThe example data of the standard deviation for gene expression levels
- puma::hgu95aphisEstimated parameters of the distribution of phi
- PureCN::centromeresA list of data.frames containing centromere positions.
- PureCN::purecn.DNAcopy.bdryDNAcopy boundary data
- PureCN::purecn.example.outputExample output
- pwalign::BLOSUM100Predefined scoring matrices
- pwalign::BLOSUM45Predefined scoring matrices
- pwalign::BLOSUM50Predefined scoring matrices
- pwalign::BLOSUM62Predefined scoring matrices
- pwalign::BLOSUM80Predefined scoring matrices
- pwalign::PAM120Predefined scoring matrices
- pwalign::PAM250Predefined scoring matrices
- pwalign::PAM30Predefined scoring matrices
- pwalign::PAM40Predefined scoring matrices
- pwalign::PAM70Predefined scoring matrices
- pwalign::phiX174PhageVersions of bacteriophage phiX174 complete genome and sample short reads
- pwalign::quPhiX174Versions of bacteriophage phiX174 complete genome and sample short reads
- pwalign::srPhiX174Versions of bacteriophage phiX174 complete genome and sample short reads
- pwalign::wtPhiX174Versions of bacteriophage phiX174 complete genome and sample short reads
- qcmetrics::psm15N example data
- QDNAseq::LGG150LGG150 chromosomes 7-10
- QFeatures::feat1Feature example data
- QFeatures::feat2Feature example data
- QFeatures::feat3Example 'QFeatures' object after processing
- QFeatures::ft_naFeature example data
- QFeatures::hlpsmshyperLOPIT PSM-level expression data
- QFeatures::se_na2Feature example data
- qmtools::faahko_seFAAH knockout LC/MS data SummarizedExperiment
- qpcrNorm::qpcrBatch.objectqpcrBatch instance qpcrBatch.object
- qpgraph::filtered.regulon6.1Preprocessed microarray oxygen deprivation data and filtered RegulonDB data
- qpgraph::gds680.esetPreprocessed microarray oxygen deprivation data and filtered RegulonDB data
- qpgraph::subset.filtered.regulon6.1Preprocessed microarray oxygen deprivation data and filtered RegulonDB data
- qpgraph::subset.gds680.esetPreprocessed microarray oxygen deprivation data and filtered RegulonDB data
- qPLEXanalyzer::ER_ARID1A_KO_MCF7ER_ARID1A_KO_MCF7 dataset
- qPLEXanalyzer::exp2_Xlinkexp2_Xlink dataset
- qPLEXanalyzer::exp3_OHT_ESR1exp3_OHT_ESR1 dataset
- qPLEXanalyzer::human_annohuman_anno dataset
- qPLEXanalyzer::mouse_annomouse_anno dataset
- qsmooth::gc
- qsvaR::covComb_tx_degRSE object of RNA-seq data that serves as output for degradation analysis
- qsvaR::degradation_tstatsDegradation time t-statistics
- qsvaR::transcriptsTranscripts for Degradation Models
- quantiseqr::dataset_racleAn exemplary dataset with samples from four patients with metastatic melanoma
- quantiseqr::ti_quant_sim1700mixturesquanTIseq output for the simulation data of 1700 mixtures for RNA-seq data
- quantro::flowSortedA subset of FlowSorted.DLPFC.450k data set
- quantsmooth::affy.cnExample data from several quantitative genomic methods
- quantsmooth::affy.posExample data from several quantitative genomic methods
- quantsmooth::bac.cnExample data from several quantitative genomic methods
- quantsmooth::bac.posExample data from several quantitative genomic methods
- quantsmooth::chrom.bandsDataset of human chromosomes and their banding patterns
- quantsmooth::chrom.bands.hg18Dataset of human chromosomes and their banding patterns
- quantsmooth::chrom.bands.hg19Dataset of human chromosomes and their banding patterns
- quantsmooth::chrom.bands.hg38Dataset of human chromosomes and their banding patterns
- quantsmooth::chrom.bands.mm10Dataset of human chromosomes and their banding patterns
- quantsmooth::ill.cnExample data from several quantitative genomic methods
- quantsmooth::ill.posExample data from several quantitative genomic methods
- qusage::BTM.geneSetsExample Gene Sets
- qusage::ISG.geneSetExample Gene Sets
- qusage::MSIG.geneSetsExample Gene Sets
- qusage::eset.fullExample gene expression set
- qusage::flu.metaExample gene expression set
- qusage::fluVaccineGene expression sets from Flu Vaccine trials
- qvalue::hedenfalkP-values and test-statistics from the Hedenfalk et al. (2001) gene expression dataset
- R3CPET::ChromosomsHuman chromosom lenghts
- R3CPET::PPI.BiogridBiogrid Network
- R3CPET::PPI.HPRDHPRD protein interaction Network
- R3CPET::RPKMSA gene expression dataset
- R3CPET::geneLocations.nucleusNucleus located genes
- r3Cseq::Myb_prom_FBMyb_prom_FB a data set for the example of r3Cseq analysis
- r3Cseq::Myb_prom_FLMyb_prom_FL a data set for the example of r3Cseq analysis
- R453Plus1Toolbox::avaSetExampleAmplicon Variant Analyzer data import
- R453Plus1Toolbox::avaSetFilteredAmplicon Variant Analyzer data import
- R453Plus1Toolbox::avaSetFiltered_annotAVASet variant annotations
- R453Plus1Toolbox::breakpointsPutative breakpoints of chimeric reads
- R453Plus1Toolbox::captureArrayCustom capture array design
- R453Plus1Toolbox::mapperSetExampleGS Reference Mapper data import
- R453Plus1Toolbox::mutationInfoExample data for 'plotVariants'
- R453Plus1Toolbox::regionsExample data for 'plotVariants'
- R453Plus1Toolbox::variantsExample data for 'plotVariants'
- R4RNA::fastaHelices predicted by TRANSAT with p-values
- R4RNA::helixHelices predicted by TRANSAT with p-values
- R4RNA::knownHelices predicted by TRANSAT with p-values
- RAIDS::demoKnownSuperPop1KGThe known super population ancestry of the demo 1KG reference profiles.
- RAIDS::demoPCA1KGThe PCA results of the demo 1KG reference dataset for demonstration purpose. Beware that the PCA has been run on a very small subset of the 1KG reference dataset and should not be used to call ancestry inference on a real profile.
- RAIDS::demoPCASyntheticProfilesThe PCA result of demo synthetic profiles projected on the demo subset 1KG reference PCA.
- RAIDS::demoPedigreeEx1The pedigree information about a demo profile called 'ex1'.
- RAIDS::matKNNSyntheticA small 'data.frame' containing the inferred ancestry on the synthetic profiles.
- RAIDS::pedSyntheticA small 'data.frame' containing the information related to synthetic profiles. The ancestry of the profiles used to generate the synthetic profiles must be present.
- RAIDS::snpPositionDemoA small 'data.frame' containing the SNV information.
- rain::menetRNASeqMouseLiverTime courses of gene expression in mouse liver
- ramr::ramr.dataSimulated Illumina HumanMethylation 450k data set with 3000 CpGs and 100 samples
- ramr::ramr.samplesSimulated Illumina HumanMethylation 450k data set with 3000 CpGs and 100 samples
- ramr::ramr.tp.nonuniqueSimulated Illumina HumanMethylation 450k data set with 3000 CpGs and 100 samples
- ramr::ramr.tp.uniqueSimulated Illumina HumanMethylation 450k data set with 3000 CpGs and 100 samples
- randPack::CT1demonstration data for use with randPack
- randPack::SampleDataRandomly generated data representing a potential patient cohort.
- randPack::alltabsdemonstration data for use with randPack
- randPack::pD1demonstration data for use with randPack
- randPack::scodemonstration data for use with randPack
- RankProd::BiomMetabolomics data on spiked apples
- RankProd::apples.clMetabolomics data on spiked apples
- RankProd::apples.dataMetabolomics data on spiked apples
- RankProd::apples.data.vsnMetabolomics data on spiked apples
- RankProd::arabGenomic Response to Brassinosteroid in Arabidopsis
- RankProd::arab.clGenomic Response to Brassinosteroid in Arabidopsis
- RankProd::arab.gnamesGenomic Response to Brassinosteroid in Arabidopsis
- RankProd::arab.originGenomic Response to Brassinosteroid in Arabidopsis
- RankProd::golubA subset of the Gene expression dataset from Golub et al. (1999)
- RankProd::golub.clA subset of the Gene expression dataset from Golub et al. (1999)
- RankProd::golub.gnamesA subset of the Gene expression dataset from Golub et al. (1999)
- RankProd::lym.expSubset of the Intensity data for 8 cDNA slides with CLL and DLBL samples from the Alizadeh et al. paper in Nature 2000
- RankProd::mzMetabolomics data on spiked apples
- RankProd::rtMetabolomics data on spiked apples
- RAREsim::afs_afrAfrican/African American target data from gnomAD v2.1 (Karczewski, 2020)
- RAREsim::nvariant_afrAfrican target data for the Number of Variants function from gnomADv2.1 (Karczewski, 2020)
- RbcBook1::bcr.corIllustrative datasets for distance measures
- RbcBook1::bcr.eucIllustrative datasets for distance measures
- RbcBook1::bcr.kldistIllustrative datasets for distance measures
- RbcBook1::bcr.manIllustrative datasets for distance measures
- RbcBook1::bcr.miIllustrative datasets for distance measures
- RbcBook1::bcr.spearIllustrative datasets for distance measures
- RbcBook1::bcr.tauIllustrative datasets for distance measures
- RbcBook1::performanceResults of tedious computations for computational inference
- RbcBook1::performanceResults of tedious computations for computational inference
- RbcBook1::performanceResults of tedious computations for computational inference
- RBGL::FileDepFileDep: a graphNEL object representing a file dependency dataset example in boost graph library
- rBiopaxParser::biopaxBiopax example data set
- rBiopaxParser::biopaxLevel3ExampleBiopax example data set
- RBM::ovarian_cancer_methylationovarian cancer methylation example from United Kingdom Ovarian Cancer Population Study (UKOPS)
- rbsurv::gliomaSetGene expression and survival data of the patients with gliomas
- RCAS::gffSample GFF file imported as a GRanges object
- RCAS::queryRegionsSample BED file imported as a GRanges object
- RCASPAR::BergamaschiGene expression data of 82 patients with 10 genes as covariates
- RCASPAR::survDataSurvial data of 82 patients
- rcellminer::Drug_MOA_KeyA data frame with descriptive information for all compound mechanism of action (MOA) abbreviations used in CellMiner.
- rCGH::agilentDBaCGH Agilent Probes GC Fraction
- rCGH::hg18Hg18 Chromosome Lengths and Centromere Locations
- rCGH::hg19Hg19 Chromosome Lengths and Centromere Locations
- rCGH::hg38Hg38 Chromosome Lengths and Centromere Locations
- RcisTarget::dbRegionsLoc_hg19_v9Genomic location for the database regions
- RcisTarget::motifAnnotationsAnnotations of Motifs to TFs
- RcisTarget::motifAnnotationsAnnotations of Motifs to TFs
- RcisTarget::motifAnnotationsAnnotations of Motifs to TFs
- RcisTarget::motifAnnotations_dmel_v8Annotations of Motifs to TFs
- RcisTarget::motifAnnotations_dmel_v9Annotations of Motifs to TFs
- RcisTarget::motifAnnotations_hgnc_v9Annotations of Motifs to TFs
- RcisTarget::motifAnnotations_mgi_v9Annotations of Motifs to TFs
- RCM::ZellerMicrobiomes of colorectal cancer patients and healthy controls
- Rcpi::AA2DACOR2D Autocorrelations Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AA3DMoRSE3D-MoRSE Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AAACFAtom-Centred Fragments Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AABLOSUM100BLOSUM100 Matrix for 20 Amino Acids
- Rcpi::AABLOSUM45BLOSUM45 Matrix for 20 Amino Acids
- Rcpi::AABLOSUM50BLOSUM50 Matrix for 20 Amino Acids
- Rcpi::AABLOSUM62BLOSUM62 Matrix for 20 Amino Acids
- Rcpi::AABLOSUM80BLOSUM80 Matrix for 20 Amino Acids
- Rcpi::AABurdenBurden Eigenvalues Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AACPSACPSA Descriptors for 20 Amino Acids calculated by Discovery Studio
- Rcpi::AAConnConnectivity Indices Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AAConstConstitutional Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AADescAllAll 2D Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AAEdgeAdjEdge Adjacency Indices Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AAEigIdxEigenvalue-Based Indices Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AAFGCFunctional Group Counts Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AAGETAWAYGETAWAY Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AAGeomGeometrical Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AAInfoInformation Indices Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AAMOE2D2D Descriptors for 20 Amino Acids calculated by MOE 2011.10
- Rcpi::AAMOE3D3D Descriptors for 20 Amino Acids calculated by MOE 2011.10
- Rcpi::AAMetaInfoMeta Information for the 20 Amino Acids
- Rcpi::AAMolPropMolecular Properties Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AAPAM120PAM120 Matrix for 20 Amino Acids
- Rcpi::AAPAM250PAM250 Matrix for 20 Amino Acids
- Rcpi::AAPAM30PAM30 Matrix for 20 Amino Acids
- Rcpi::AAPAM40PAM40 Matrix for 20 Amino Acids
- Rcpi::AAPAM70PAM70 Matrix for 20 Amino Acids
- Rcpi::AARDFRDF Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AARandicRandic Molecular Profiles Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AATopoTopological Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AATopoChgTopological Charge Indices Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AAWHIMWHIM Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AAWalkWalk and Path Counts Descriptors for 20 Amino Acids calculated by Dragon
- Rcpi::AAindexAAindex Data of 544 Physicochemical and Biological Properties for 20 Amino Acids
- RCSL::annCell type annotations of 'yan' datasets by Yan et al.
- RCSL::yanA public scRNA-seq dataset by Yan et al.
- REBET::genotypesData for the example
- REBET::responseData for the example
- REBET::subRegionsData for the example
- receptLoss::nhrsTable of Nuclear Hormone Receptors (NHRs)
- reconsi::VandeputteMicrobiomes of Crohn's disease patients and healthy controls
- recount::recount_abstractSummary information at the project level for the recount project
- recount::recount_exonsExon annotation used in recount
- recount::recount_genesGene annotation used in recount
- recount::recount_urlFiles and URLs hosted by the recount project
- recount::rse_gene_SRP009615RangedSummarizedExperiment at the gene level for study SRP009615
- recoup::test.designReference and genomic sample regions for recoup testing
- recoup::test.exonsReference and genomic sample regions for recoup testing
- recoup::test.genomeReference and genomic sample regions for recoup testing
- recoup::test.inputReference and genomic sample regions for recoup testing
- RedeR::ER.limmaPre-processed dataset for RedeR case studies.
- RedeR::hs.interPre-processed igraph object for RedeR case studies.
- REDseq::example.REDseqan example sequencing dataset from a restoration enzyme digestion (RED) experiment
- REDseq::example.assignedREDseqan example assigned REDseq dataset
- REDseq::example.mapan example REmap dataset
- RegEnrich::Lyme_GSE63085Example RNAseq dataset [Human]
- RegEnrich::TFsHuman gene regulators
- RegionalST::exampleResExample DE output
- RegionalST::example_sceExample single cell experiment for input
- RegionalST::pathways_hallmarkHallmark database
- RegionalST::pathways_keggKEGG database
- RegionalST::pathways_reactomeREACTOME database
- regioneReloaded::AlienGenomeAlienGenome
- regioneReloaded::AlienRSList_broadAlienRSList_broad
- regioneReloaded::AlienRSList_narrowAlienRSList_narrow
- regioneReloaded::cw_Alien_RaRcw_Alien_RaR
- regioneReloaded::cw_Alien_ReGcw_Alien_ReG
- regioneReloaded::cw_Alien_ReG_no_Squarecw_Alien_ReG_no_Square
- regioneReloaded::cw_Alien_ReRcw_Alien_ReR
- regioneReloaded::mLZ_regA_ReGmLZ_regA_ReG
- regioneReloaded::mLZ_regA_ReG_brmLZ_regA_ReG_br
- regioneReloaded::mLZ_regD_ReGmLZ_regD_ReG
- REMP::Alu.hg19.demoSubset of Alu genomic location dataset (hg19)
- REMP::Alu.hg38.demoSubset of Alu genomic location dataset (hg38)
- Repitools::chr21genesPositions of Genes on Human Chromosome 21
- Repitools::exprVector of expression differences
- Repitools::samplesListShort Reads from Cancer and Normal
- ReportingTools::mockRnaSeqDataA counts table of mock RNA-deq data in mouse.
- RESOLVE::backgroundGermline replication error
- RESOLVE::background2COSMIC replication error
- RESOLVE::cn_example_reducedA reduced version of the copy number data for 5 TCGA samples in the format compatible with the import function
- RESOLVE::id_example_reducedA reduced version of the indel data for 3 samples in the format compatible with the import function
- RESOLVE::patientsPoint mutations for 560 breast tumors
- RESOLVE::plot_data_examplesList data structure to run examples
- RESOLVE::ssm560_reducedA reduced version of the point mutations for 560 breast tumors in the format compatible with the import function
- retrofit::testSimulationDatasimulation data
- retrofit::vignetteColonDatacolon vignette
- retrofit::vignetteSimulationDatasimulation vignette
- rexposome::ex_imp'imExposomeSet' for testing purpouses
- rexposome::expo'ExposomeSet' for testing purpouses
- rexposome::expo_c'ExposomeClust' for testing purpouses
- rexposome::me'data.frame' for testing purpouses
- rfPred::example_GRangesToy example of GRanges object
- rfPred::variant_list_YToy example of data.frame
- RGSEA::cmapData from Connectivity map build 01
- RGSEA::e1Data from GDS4102
- RGSEA::e2Data from GDS4100
- rgsepd::IlluminaBodymapSample RNA-Seq Counts data
- rgsepd::IlluminaBodymapMetaMetadata table for the included sample data
- RiboDiPA::data.binnedAn example of binned P-sites data
- RiboDiPA::data.psiteAn example of P-site coverage data
- RiboDiPA::result.exonAn example of exon-level differential pattern analysis result
- RiboDiPA::result.pstAn example of differential pattern analysis result
- RiboProfiling::cdsPosTranscPer transcript relative position of start and end codons for dataset ctrlGAlignments
- RiboProfiling::codonDataCtrlCodon frequency and coverage in ORFs on chromosome 1, for dataset ctrlGAlignments
- RiboProfiling::codonIndexCovCtrlThe read coverage for each codon in ORFs on chromosome 1, for dataset ctrlGAlignments
- RiboProfiling::ctrlGAlignmentsRibosome profiling data on chr1 in human primary BJ fibroblasts control data: PMID: 23594524.
- rifi::example_input_e_coliAn example SummarizedExperiment from E. coli An example SummarizedExperiment from RNA-seq containing information about the intensities at all time points (assay). Seqnames, IRanges and strand columns (rowRanges)and colData with time point series and replicates.
- rifi::example_input_minimalAn artificial example SummarizedExperiment An example SummarizedExperiment containing information about the intensities at all time points (assay). Seqnames, IRanges and strand columns (rowRanges) and colData with time point series and replicates.
- rifi::example_input_synechocystis_6803An example input data frame from Synechocystis PCC 6803 A SummarizedExperiment from microarrays data containing information about the intensities at all time points (assay), Seqnames, IRanges and strand columns (rowRanges) and colData with time point series and averaged replicates.
- rifi::fit_e_coliThe result of rifi_fit for E.coli example data A SummarizedExperiment containing the output from rifi_fit as an extension of rowRanges and metadata.
- rifi::fit_minimalThe artificial result of rifi_fit for artificial example data A SummarizedExperiment containing the output from rifi_fit.
- rifi::fit_synechocystis_6803The result of rifi_fit for Synechocystis 6803 example data A SummarizedExperiment containing the output from rifi_fit as an extension of rowRanges and metadata.
- rifi::fragmentation_e_coliThe result of rifi_fragmentation for E.coli example data A SummarizedExperiment containing the output from rifi_fragmentation as an extension of rowRanges
- rifi::fragmentation_minimalThe result of rifi_fragmentation for artificial example data A SummarizedExperiment containing the output from rifi_fragmentation as an extension of rowRanges and metadata.
- rifi::fragmentation_synechocystis_6803The result of rifi_fragmentation for Synechocystis 6803 example data A SummarizedExperiment containing the output from rifi_fragmentation as an extension fo rowRanges
- rifi::penalties_e_coliThe result of rifi_penalties for E.coli example data. A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata.
- rifi::penalties_minimalThe result of rifi_penalties for artificial example data A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata.
- rifi::penalties_synechocystis_6803The result of rifi_penalties for Synechocystis 6803 example data. A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata.
- rifi::preprocess_e_coliThe result of rifi_preprocess for E.coli example data A SummarizedExperiment containing the output from rifi_penalties including the logbook and the four penalty objects as metadata. A list containing the output from rifi_preprocess, including the inp and the modified input_df.
- rifi::preprocess_minimalThe result of rifi_preprocess for artificial example data A SummarizedExperiment containing the output from rifi_preprocess
- rifi::preprocess_synechocystis_6803The result of rifi_preprocess for Synechocystis 6803 example data is a A SummarizedExperiment containing the output of rifi_preprocess as an extention to rowRanges
- rifi::res_minimalThe result of event_dataframe for E.coli artificial example. A data frame combining the processed genome annotation and a SummarizedExperiment data from rifi_stats. The dataframe is
- rifi::stats_e_coliThe result of rifi_stats for E.coli example data A SummarizedExperiment containing the output from rifi_stats
- rifi::stats_minimalThe result of rifi_stats for artificial example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges and metadata (gff file processed, see gff file documentation)
- rifi::stats_synechocystis_6803The result of rifi_stats for Synechocystis 6803 example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges
- rifi::summary_e_coliThe result of rifi_summary for E.coli example data A SummarizedExperiment containing the output of rifi_stats as an extention to rowRanges
- rifi::summary_minimalThe result of rifi_summary for artificial example data A SummarizedExperiment with the output from rifi_summary as metadata
- rifi::summary_synechocystis_6803The result of rifi_summary for Synechocystis 6803 example data A list containing the output from rifi_summary, including the fragment based data frame, bin based data frame, event data frame and the TI dataframe.
- rifi::wrapper_e_coliThe result of rifi_wrapper for E.coli example data A list of SummarizedExperiment containing the output of rifi_wrapper. The list contains 6 elements of SummarizedExperiment output of rifi_preprocess, rifi_fit, rifi_penalties, rifi_fragmentation, rifi_stats and rifi_summary. The plot is generated from rifi_visualization. for more detail, please refer to each function separately.
- rifi::wrapper_minimalThe result of rifi_wrapper for E.coli artificial example. A list of SummarizedExperiment containing the output of rifi_wrapper. The list contains 6 elements of SummarizedExperiment output of rifi_preprocess, rifi_fit, rifi_penalties, rifi_fragmentation, rifi_stats and rifi_summary. The plot is generated from rifi_visualization. for more detail, please refer to each function separately.
- rifi::wrapper_summary_synechocystis_6803The result of rifi_wrapper for summary_synechocystis_6803 example data A list of SummarizedExperiment containing the output of rifi_wrapper. The list contains 6 elements of SummarizedExperiment output of rifi_preprocess, rifi_fit, rifi_penalties, rifi_fragmentation, rifi_stats and rifi_summary. The plot is generated from rifi_visualization. for more detail, please refer to each function separately.
- rifiComparative::annot_gThe result of gff3_preprocessing of gff3 file A list containing all necessary information from a gff file for adjusting_HLToInt and visualization.
- rifiComparative::data_combined_minimalThe result of joining_by_row for inp_s and inp_f example data A data frame containing the output of joining_by_row as a data frame
- rifiComparative::df_comb_minimalThe result of joining_by_column for data_combined_minimal example data A data frame containing the output of joining_by_row as a data frame
- rifiComparative::df_mean_minimalThe result of adjusting_HLToInt for stats_df_comb_minimal and annotation example data A data frame containing the output of adjusting_HLToInt as a data frame
- rifiComparative::differential_expressionAn example data frame from Synechosystis PCC 6803 differential probes expression obtained from limma package and only interesting variables were selected. The data frame was used entirely.
- rifiComparative::fragment_intThe result of fragmentation for df_comb_minimal example data A data frame containing the output of fragmentation as a data frame
- rifiComparative::inp_fThe result of loading_fun for stats_se_cdt2 example data Two data frame containing the output of loading_fun as second element of a list.
- rifiComparative::inp_sThe result of loading_fun for stats_se_cdt1 example data Two data frame containing the output of loading_fun as first element of a list.
- rifiComparative::pen_HLThe result of penalties for df_comb_minimal example data. A list containing the output from penalties including the logbook and two penalty objects.
- rifiComparative::pen_intThe result of penalties for df_comb_minimal example data. A list containing the output from penalties including the logbook and two penalty objects.
- rifiComparative::penalties_dfThe result of penalties for df_comb_minimal example data A data frame containing the output of penalties as a data frame
- rifiComparative::stats_df_comb_minimalThe result of statistics for fragment_int example data A data frame containing the output of statistics as a data frame
- rifiComparative::stats_se_cdt1An example SummarizedExperiment from Synechosystis PCC 6803 first condition obtained from rifi_statistics and used as input for rifiComparative
- rifiComparative::stats_se_cdt2An example SummarizedExperiment from Synechosystis PCC 6803 second condition obtained from rifi_statistics and used as input for rifiComparative
- RITAN::vac1.day0vs31.de.genesThis dataset is included as an example in the package:
- RITAN::vac1.day0vs56.de.genesThis dataset is included as an example in the package:
- RITAN::vac2.day0vs31.de.genesThis dataset is included as an example in the package:
- RITAN::vac2.day0vs56.de.genesThis dataset is included as an example in the package:
- RJMCMCNucleosomes::RJMCMC_resultNucleosomes obtained by running RJMCMC function using reads from reads_demo_02 dataset (for demo purpose).
- RJMCMCNucleosomes::reads_demo_01Forward reads and reverse reads in 'GRanges' format (for demo purpose).
- RJMCMCNucleosomes::reads_demo_02Forward reads and reverse reads in 'GRanges' format (for demo purpose).
- RJMCMCNucleosomes::syntheticNucleosomeReadsSimulated dataset of reads generated by 'nucleoSim' package (for demo purpose).
- RLassoCox::dGMMirGraphThe KEGG network
- RLassoCox::mRNA_matrixThe expression data
- RLassoCox::survDataSurvival data
- Rmagpie::vV70genesvV70genes: van't Veer et al. 70 best genes in an object of class dataset.
- RNAAgeCalc::fpkmAn example of FPKM data
- RNAAgeCalc::rawcountAn example of RNASeq counts data
- RNAdecay::RPMsRNA abundance reads per million over RNA decay timecourse
- RNAdecay::decay_dataNormalized RNA abundance RNA decay timecourse
- RNAdecay::modelsExample double exponential decay modeling results
- RNAdecay::resultsExample double exponential decay modeling results
- rnaEditr::rnaedit_dfExample breast cancer RNA editing dataset.
- rnaEditr::t_rnaedit_dfTransposed breast cancer example dataset.
- RNAmodR::csdExample data in the RNAmodR package
- RNAmodR::e3sdExample data in the RNAmodR package
- RNAmodR::e5sdExample data in the RNAmodR package
- RNAmodR::esdExample data in the RNAmodR package
- RNAmodR::msiExample data in the RNAmodR package
- RNAmodR::ne3sdExample data in the RNAmodR package
- RNAmodR::ne5sdExample data in the RNAmodR package
- RNAmodR::pesdExample data in the RNAmodR package
- RNAmodR::psdExample data in the RNAmodR package
- RNAmodR::sdlExample data in the RNAmodR package
- RNAmodR::sdsExample data in the RNAmodR package
- RNAmodR.AlkAnilineSeq::msaasExample data in the RNAmodR.AlkAnilineSeq package
- RNAmodR.ML::dmodExample data in the RNAmodR.ML package
- RNAmodR.ML::meExample data in the RNAmodR.ML package
- RNAmodR.ML::mod7Example data in the RNAmodR.ML package
- RNAmodR.ML::modelExample data in the RNAmodR.ML package
- RNAmodR.RiboMethSeq::msrmsExample data in the RNAmodR.RiboMethSeq package
- RNAsense::MZsoxTime resolved RNA seq data for early zygotic development of zebra fish.
- rnaseqcomp::simdataExample of Quantifications on Simulation Data
- RNAseqCovarImpute::example_DGESimulated counts in DGE list
- RNAseqCovarImpute::example_dataSimulated dataset
- RnBeads::lump.hg19LUMP Support
- RnBeads::lump.hg38LUMP Support (hg38)
- Rnits::yeastchemostatYeast chemostat data from Ronen and Botstein (Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):389-94. Epub 2005 Dec 28.)
- roastgsa::dragtabledragtable for html writings
- roastgsa::expr.tcgaTumor Bladder TCGA data
- roastgsa::fd.tcgaTumor Bladder TCGA data
- roastgsa::hallmarks.hsHallmarks homo sapiens gene symbol
- roastgsa::kegg.hsKEGG genesets homo sapiens entrez
- roastgsa::pd.tcgaTumor Bladder TCGA data
- roastgsa::sorttablesorttable for html writings
- RolDE::data1A proteomics dataset with random protein expression values - no missing values.
- RolDE::data2A small dataset with 50 proteins and 30 samples for the example usage of RolDE
- RolDE::data3A semi-simulated UPS1 spike-in dataset with differences in longitudinal expression for the spike-in proteins - no missing values.
- RolDE::des_matrix1A RolDE design matrix for data1
- RolDE::des_matrix2A RolDE design matrix for data2
- RolDE::des_matrix3A RolDE design matrix for data3
- RolDE::res1RolDE results for data1
- RolDE::res3RolDE results for data3
- ropls::NCI60Microarray gene expression profiles of the NCI 60 cell lines from 4 different platforms
- ropls::aminoacidsAmino-Acids Dataset
- ropls::celluloseNIR-Viscosity example data set to illustrate multivariate calibration using PLS, spectral filtering and OPLS
- ropls::cornellOctane of various blends of gasoline
- ropls::foodsFood consumption patterns accross European countries (FOODS)
- ropls::linnerudLinnerud Dataset
- ropls::lowarpA multi response optimization data set (LOWARP)
- ropls::mark'mark' Dataset
- ropls::sacurineAnalysis of the human adult urinary metabolome variations with age, body mass index and gender
- ROSeq::L_Tung_singleSingle cell samples for DE genes analysis
- ROTS::affySpikeInGene expression data from the Affymetrix spike-in experiment
- ROTS::affySpikeIn.LGene expression data from the Affymetrix spike-in experiment
- ROTS::affySpikeIn.gnamesGene expression data from the Affymetrix spike-in experiment
- ROTS::spikedgeneGene expression data from the Affymetrix spike-in experiment
- ROTS::upsSpikeInProtein expression data from the CPTAC Technology Assessment (Study 6)
- rprimer::exampleRprimerAlignmentExample datasets
- rprimer::exampleRprimerAssayExample datasets
- rprimer::exampleRprimerMatchAssayExample datasets
- rprimer::exampleRprimerMatchOligoExample datasets
- rprimer::exampleRprimerOligoExample datasets
- rprimer::exampleRprimerProfileExample datasets
- RRHO::HNPRRHO comparison data sets.
- RRHO::MyRRHO comparison data sets.
- RRHO::SestanRRHO comparison data sets.
- rsemmed::g_miniExample data for the rsemmed package
- rsemmed::g_smallExample data for the rsemmed package
- RSVSim::segDupsSegmental duplications
- RSVSim::weightsMechanismsWeights for SV formation mechanisms
- RSVSim::weightsRepeatsWeights for repeat region bias
- RTCGAToolbox::accminiA subset of the Adrenocortical Carcinoma (ACC) dataset
- RTN::pksDataPre-processed datasets for the RTN package.
- RTN::stniA pre-processed TNI for demonstration purposes only.
- RTN::tfsDataPre-processed datasets for the RTN package.
- RTN::tnaDataPre-processed datasets for the RTN package.
- RTN::tniDataPre-processed datasets for the RTN package.
- RTNsurvival::survival.dataA pre-processed dataset for demonstration purposes only.
- RTopper::datA test dataset for the RTopper package
- RTopper::fgsListA list of Functional Gene Set (FGS) to be used to run the examples in the RTopper package
- RTopper::gseResultsSepA list of separated gene set enrichment p-values to be used to run the examples in the RTopper package
- RTopper::intScoresA list of genomic scores integrated across distinct data sets to be used to run the examples in the RTopper package
- RTopper::phenoA test dataset for the RTopper package
- RTopper::sepScoresA list of separate gene-to-phenotype association scores, obtained indipendently for each distinct data set to be used to run the examples in the RTopper package
- Rtpca::ori_et_al_complex_ppisData frame of eukaryotic protein-protein interactions inferred from annotated protein complexes by Ori et al. and StringDB interations with a combined score of at least 900
- Rtpca::ori_et_al_complexes_dfData frame of annotated protein complexes by Ori et al.
- Rtpca::string_ppi_dfData frame of annotated human protein-protein interactions retrieved from stringDB with a combined interaction score equal or higher than 700
- rtracklayer::cpneTrackCPNE1 SNP track
- rtracklayer::targetsmicroRNA target sites
- Rtreemix::hiv.dataExample of an RtreemixData object
- rTRM::biogrid_hsNetwork dataset of class 'igraph'
- rTRM::biogrid_mmNetwork dataset of class 'igraph'
- RVS::ex.ped.matmatrix of pedigree information and genotype data from famVCF stored in the LINKAGE format
- RVS::fam15157.vcfVCF objects containing genotype data for two families: fam15157 and fam28003 (corresponding to the secondCousinTriple and firstAndSecondCousinsTriple families in samplePedigrees)
- RVS::fam28003.vcfVCF objects containing genotype data for two families: fam15157 and fam28003 (corresponding to the secondCousinTriple and firstAndSecondCousinsTriple families in samplePedigrees)
- RVS::samplePedigreeslist of 8 sample pedigree objects
- RVS::snpMatSnpMatrix with genotype information from famVCF for fam15157
- safe::p53.statp53 Mutation Status
- sagenhaft::SAGEartifactsFunctions for SAGE library extraction
- sangeranalyseR::qualityReportDataQualityReport instance
- sangeranalyseR::sangerAlignmentDataSangerAlignment instance
- sangeranalyseR::sangerContigDataSangerContig instance
- sangeranalyseR::sangerReadFDataSangerRead instance
- SANTA::edgelist.humannetPre-processed dataset for the SANTA vignette
- SANTA::edgelist.intactPre-processed dataset for the SANTA vignette
- SANTA::g.bandyopadhyay.treatedPre-processed dataset for the SANTA vignette
- SANTA::g.bandyopadhyay.untreatedPre-processed dataset for the SANTA vignette
- SANTA::g.costanzo.corPre-processed dataset for the SANTA vignette
- SANTA::g.costanzo.rawPre-processed dataset for the SANTA vignette
- SANTA::g.srivas.highPre-processed dataset for the SANTA vignette
- SANTA::g.srivas.untreatedPre-processed dataset for the SANTA vignette
- SANTA::go.entrezPre-processed dataset for the SANTA vignette
- SANTA::rnai.cheungPre-processed dataset for the SANTA vignette
- SARC::test_cnvtest cnv
- SARC::test_cnv2test cnv 2
- SARC::test_covtest coverage file
- sarks::simulatedScoresScores associated with simulated sequences from SArKS paper.
- sarks::simulatedSeqsSimulated sequences from SArKS paper.
- saseR::ASpliSEASpliSE
- saseR::SEbinsSEbins
- saseR::SEgenesSEgenes
- saseR::SEjunctionsSEjunctions
- saseR::featuresfeatures
- satuRn::Tasic_counts_vignetteA 'Matrix' with transcript-level counts derived from our case study which builds on the dataset of Tasic et al. We used Salmon (V1.1.0) to quantify all L5IT cells (both for ALM and VISp tissue) from mice with a normal eye condition. From these cells, we randomly sampled 20 cells of each of the following cell types to use for this vignette; L5_IT_VISp_Hsd11b1_Endou, L5_IT_ALM_Tmem163_Dmrtb1 and L5_IT_ALM_Tnc. The data has already been leniently filtered with the 'filterByExpr' function of edgeR.
- satuRn::Tasic_metadata_vignetteMetadata associated with the expression matrix 'Tasic_counts_vignette'. See '?Tasic_counts_vignette' for more information on the dataset.
- satuRn::sumExp_exampleA 'SummarizedExperiment' derived from our case study which builds on the dataset of Tasic et al. It contains the same cells as the data object used in the vignette (see '?Tasic_counts_vignette' for more information). In this SummarizedExperiment, we performed a filtering with 'filterByExpr' of edgeR with more stringent than default parameter settings (min.count = 100,min.total.count = 200, large.n = 50, min.prop = 0.9) to reduced the number of retained transcripts. We used this object to create an executable example in the help files of satuRn.
- SBGNview::SBGNhub.id.mapping.tablesMapping tables available in SBGNhub
- SBGNview::mapped.idsIDs mappable by SBGNview
- SBGNview::pathways.infoInformation of collected pathways
- SBGNview::pathways.statsNumber of pathways collected
- SC3::annCell type annotations for data extracted from a publication by Yan et al.
- SC3::yanSingle cell RNA-Seq data extracted from a publication by Yan et al.
- Scale4C::liverDataExample 4C-seq data set of fetal liver data
- Scale4C::liverDataVPExample 4C-seq data set of fetal liver data, with added VP
- scanMiR::SampleKdModelExample KdModel (hsa-miR-155-5p)
- scanMiR::SampleTranscriptExample transcript sequence
- scAnnotatR::tirosh_mel80_exampleA Seurat Object Sample
- SCANVIS::GBMlist of 3 TCGA glioblastoma samples, parts thereof, outputs of SCANVISscan and SCANVISlinkvar functions with toy variants supplied for the variant-SJ mapping
- SCANVIS::LUADlist of 3 TCGA lung adenocarcinoma samples, parts thereof, outputs of SCANVISscan
- SCANVIS::LUSClist of 3 TCGA lung squamous cell carcinoma samples, parts thereof, both outputs of SCANVISscan with the second sample being variant-mapped via SCANVISlinkvar
- SCANVIS::gbm3part of a TCGA glioblastoma sample from STAR alignment SJ.tab file
- SCANVIS::gbm3.vcfa toy set of 6 variants that pair up with the gbm3 data example
- SCANVIS::gen19parts of the annotation object created by the SCANVISannotation function when used with the url ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/ which references the gencode v19 GTF file for human hg19
- scatterHatch::pdacDataTissue-CyCIF data of Pancreatic Ductal Adenocarcinoma (PDAC)
- scBFA::celltypeCell types as labels of example scRNA-seq dataset(exprdata)
- scBFA::celltype_toytoy cell type vector with 3 cell types generated for 5 cells in toy dataset
- scBFA::disperPlotReference dataset(disperPlot)
- scBFA::exprdatascRNA-seq dataset(exprdata)
- scBFA::zinb_toyexample zinb object after fitting a toy dataset with 5 cells and 10 genes
- SCBN::orthgenesA real dataset of orthologous genes between the different species.
- SCBN::sim_dataA simulation dataset of orthologous genes between the different species.
- scBubbletree::d_500Dataset: 500 PBMCs
- scBubbletree::d_cclDataset: scRNA-seq data of 3,918 cells from 5 adenocarcinoma cell lines
- scCB2::mbrainSubSubset of 1k Brain Cells from an E18 Mouse
- scClassify::scClassify_exampleExample data used in scClassify package
- scClassify::trainClassExample_wangSubset of pretrained model of Wang et al.
- scClassify::trainClassExample_xinSubset of pretrained model of Xin et al.
- sccomp::counts_objcounts_obj
- sccomp::glm_dirichlet_multinomialglm_dirichlet_multinomial
- sccomp::glm_dirichlet_multinomial_generate_quantitiesglm_dirichlet_multinomial_generate_quantities
- sccomp::glm_dirichlet_multinomial_imputationglm_dirichlet_multinomial_imputation
- sccomp::glm_multi_betaglm_multi_beta
- sccomp::glm_multi_beta_generate_dataglm_multi_beta_generate_data
- sccomp::multipanel_thememultipanel_theme
- sccomp::sce_objsce_obj
- sccomp::seurat_objseurat_obj
- scDD::scDatExData: Toy example data
- scDD::scDatExListData: Toy example data list
- scDD::scDatExSimData: Toy example of simulated data
- scDDboost::sim_datscDDboost
- scde::es.mef.smallSample data
- scde::knnSample error model
- scde::o.ifmSample error model
- scde::pollenSample data
- scde::scde.edffInternal model data
- scDesign3::example_sceA SingelCellExperiment object containing both cell type and pseudotime
- scds::sce_chclExample single cell experiment ('SingleCellExperiment') object
- SCFA::GBMGBM
- scFeatureFilter::scData_hESCExpression data from 32 human embryonic stem cells
- scFeatures::example_scrnaseqExample of scRNA-seq data
- scFeatures::scfeatures_resultExample of scFeatures() output
- scGPS::day_2_cardio_cell_sampleOne of the two example single-cell count matrices to be used for training 'scGPS' model
- scGPS::day_5_cardio_cell_sampleOne of the two example single-cell count matrices to be used for 'scGPS' prediction
- scGPS::training_gene_sampleInput gene list for training 'scGPS', e.g. differentially expressed genes
- scHOT::MOB_subsetMOB_subset spatial example data
- scHOT::liverLiver trajectory example data
- scider::speDescription of the scider example datasets
- scmap::annCell type annotations for data extracted from a publication by Yan et al.
- scmap::yanSingle cell RNA-Seq data extracted from a publication by Yan et al.
- scMerge::example_sceSubsetted mouse ESC 'SingleCellExperiment' object
- scMerge::segListStably expressed gene list in official gene symbols for both human and mouse
- scMerge::segList_ensemblGeneIDStably expressed gene list in EnsemblGeneID for both human and mouse
- scMET::scmet_diff_dtSynthetic methylation data from two groups of cells
- scMET::scmet_dtSynthetic methylation data from a single population
- scMultiSim::GRN_params_100100_gene_GRN is a matrix of GRN params consisting of 100 genes where: # - column 1 is the target gene ID, # - column 2 is the gene ID which acts as a transcription factor for the target (regulated) gene # - column 3 is the effect of the column 2 gene ID on the column 1 gene ID
- scMultiSim::GRN_params_1139GRN_params_1139 is a matrix of GRN params consisting of 1139 genes where: # - column 1 is the target gene ID, # - column 2 is the gene ID which acts as a transcription factor for the target (regulated) gene # - column 3 is the effect of the column 2 gene ID on the column 1 gene ID
- scMultiSim::dens_nonzerothis is the density function of log(x+1), where x is the non-zero values for ATAC-SEQ data
- scMultiSim::gene_len_poola pool of gene lengths to sample from
- scMultiSim::len2nfragfrom transcript length to number of fragments (for the nonUMI protocol)
- scMultiSim::match_paramsdistribution of kinetic parameters learned from the Zeisel UMI cortex datasets
- SCnorm::ExampleSimSCDataExample datasets for SCnorm
- scone::cellcycle_genesData: Positive and Negative Control Genes
- scone::cortical_markersData: Positive and Negative Control Genes
- scone::housekeepingData: Positive and Negative Control Genes
- scone::housekeeping_revisedData: Positive and Negative Control Genes
- Sconify::bz.gmcsf.finalBodenmiller-Zunder GM-CSF post-SCONE final data
- Sconify::bz.gmcsf.final.norm.scaleBodenmiller-Zunder GM-CSF post-SCONE final data, that's been quantile normalized and z scored.
- Sconify::existRandom musing
- Sconify::funct.markersFunctional markers from the Wanderlust dataset.
- Sconify::input.markersInput markers for the Wanderlust dataset
- Sconify::markersMarkers for the Wanderlust dataset
- Sconify::wand.combinedWanderlust data combined basal and IL7 cells
- Sconify::wand.finalPost-scone output of the "combiend" Wanderlust data.
- Sconify::wand.ideal.kA named vector to help the user determine the ideal k for the Wanderlust dataset.
- Sconify::wand.il7Wanderlust IL7 data
- Sconify::wand.sconeWanderlust scone output
- SCOPE::QCmetric.scopeDemoPre-stored QCmetric data for demonstration purposes
- SCOPE::Y_simA read count matrix in the toy dataset
- SCOPE::coverageObj.scopeDemoPre-stored coverageObj.scope data for demonstration purposes
- SCOPE::iCN_simA post cross-sample segmentation integer copy number matrix returned by SCOPE in the demo
- SCOPE::normObj.scopeDemoPre-stored normObj.scope data for demonstration purposes
- SCOPE::ref.scopeDemoPre-stored 500kb-size reference genome for demonstration purposes
- SCOPE::ref_simA reference genome in the toy dataset
- scoreInvHap::RefsGenotype frequency in references
- scoreInvHap::SNPsR2R2 between the SNPs and the inversion status
- scoreInvHap::hetRefsHeterozygote genotypes in the references
- scoreInvHap::infoSNP reference description
- scoreInvHap::inversionGRInversions' description
- scp::leduc_minimalMinimally processed single-cell proteomics data set
- scp::mqScpDataExample MaxQuant/SCoPE2 output
- scp::sampleAnnotationSingle cell sample annotation
- scp::scp1Single Cell QFeatures data
- scPCA::background_dfSimulated Background Data for cPCA and scPCA
- scPCA::toy_dfSimulated Target Data for cPCA and scPCA
- scPipe::UMI_duplicationUMI duplication statistics for a small sample scRNA-seq dataset to demonstrate capabilities of scPipe
- scPipe::cell_barcode_matchingcell barcode demultiplex statistics for a small sample scRNA-seq dataset to demonstrate capabilities of scPipe
- scPipe::sc_sample_dataa small sample scRNA-seq counts dataset to demonstrate capabilities of scPipe
- scPipe::sc_sample_qcquality control information for a small sample scRNA-seq dataset to demonstrate capabilities of scPipe.
- scReClassify::gse87795_subset_sceGSE827795 subset data
- scRecover::countsscRecoverTest: A test dataset for scRecover
- scRecover::labelsscRecoverTest: A test dataset for scRecover
- scRecover::oneCellscRecoverTest: A test dataset for scRecover
- ScreenR::annotation_tableTable for the annotation of Barcode
- ScreenR::count_tableTable of the count table
- scRepertoire::contig_listA list of 8 single-cell T cell receptor sequences runs.
- scRepertoire::mini_contig_listProcessed subset of 'contig_list'
- scRepertoire::scRep_exampleA Seurat object of 500 single T cells,
- scruff::bamExampleExample GAlignments Object
- scruff::barcodeExampleA vector of example cell barcodes.
- scruff::cbtop10000Top 10,000 rows for v1, v2, and v3 cell barcode whitelist files
- scruff::sceExampleExample SingleCellExperiment Object
- scruff::validCbCell barcode whitelist (737K-august-2016.txt)
- scShapes::scDataSample data for analysis
- scTensor::GermMaleThe matrix which is used as test data of scTensor.
- scTensor::labelGermMaleThe vector contains the celltype information and color scheme of GermMale
- scTensor::mThe gene-wise mean vector of Quartz-Seq data.
- scTensor::tsneGermMaleThe result of Rtsne against GermMale
- scTensor::vThe gene-wise variance vector of Quartz-Seq data.
- scTGIF::DistalLungEpitheliumGene expression matrix of DistalLungEpithelium dataset containing five cluster.
- scTGIF::label.DistalLungEpitheliumCellular label of DistalLungEpithelium dataset containing five cluster.
- scTGIF::pca.DistalLungEpitheliumThe result of PCA of the DistalLungEpithelium dataset.
- scviR::clusters.adtADT-based cluster labels for 7472 cells in OSCA chapter 12 analysis
- scviR::clusters.rnamRNA-based cluster labels for 7472 cells in OSCA chapter 12 analysis
- SDAMS::exampleSingleCellTwo example datasets for SDAMS package
- SDAMS::exampleSumExpTwo example datasets for SDAMS package
- seahtrue::revive_output_donor_ADataset PBMC donor A
- sechm::Chen2017Example dataset
- segmenter::test_objA segmentation object generated from the test data
- segmenter::test_objsA a list of segmentation objects generated from the test data
- segmentSeq::hSLPreprocessed 'lociData' object containing likelihoods of methylation at each locus.
- SemDist::IAccrInformation Accretion Data
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- semisup::tableTable
- semisup::toydataToydata
- seq.hotSPOT::mutation_dataSingle Nucleotide Variants in Clinically-Normal Epidermis
- seq2pathway::Chipseq_Peak_demochip seq loci data example
- seq2pathway::GRanges_demoloci information with GRanges format
- seq2pathway::dat_RNARNA sequence data example
- seq2pathway::dat_chipchip seq data example
- SeqArray::KG_P1_SampDataSimulated sample data for 1000 Genomes Phase 1
- seqCAT::test_comparisonOverlapping and compared SNVs
- seqCAT::test_profile_1SNV profile 1
- seqCAT::test_profile_2SNV profile 2
- seqCAT::test_profile_3SNV profile 3
- seqCAT::test_similaritiesCollated similarities object
- seqCAT::test_variant_listModified variant list object
- SeqGate::data_MiTF_1000genesExtract of a Transciptome Dataset from Human Melanoma Cell Line
- SeqGSEA::DEscorePre-calculated DE/DS scores
- SeqGSEA::DEscore.permPre-calculated DE/DS scores
- SeqGSEA::DSscorePre-calculated DE/DS scores
- SeqGSEA::DSscore.permPre-calculated DE/DS scores
- SeqGSEA::GS_exampleSeqGeneSet object example
- SeqGSEA::RCS_exampleReadCountSet object example
- seqPattern::TBPpwmPosition-weight matrix for TATA-box binding protein motif
- seqPattern::zebrafishPromotersZebrafish promoters sequences
- seqPattern::zebrafishPromoters24hZebrafish promoters genomic coordinates
- seqsetvis::Bcell_peaks4 random peaks for paired-end data
- seqsetvis::CTCF_in_10a_bigWig_urlsFTP URL path for vignette data.
- seqsetvis::CTCF_in_10a_narrowPeak_grslist of GRanges that results in 100 random subset when overlapped
- seqsetvis::CTCF_in_10a_narrowPeak_urlsFTP URL path for vignette data. from
- seqsetvis::CTCF_in_10a_overlaps_gr100 randomly selected regions from overlapping CTCF peaks in 10a cell ChIP-seq
- seqsetvis::CTCF_in_10a_profiles_dtProfiles for 100 randomly selected regions from overlapping CTCF peaks in 10a cell ChIP-seq Results from fetching bigwigs with CTCF_in_10a_overlaps_gr.
- seqsetvis::CTCF_in_10a_profiles_grProfiles for 100 randomly selected regions from overlapping CTCF peaks in 10a cell ChIP-seq Results from CTCF_in_10a_overlaps_gr
- seqsetvis::chromHMM_demo_bw_states_grMCF10A CTCF profiles at 20 windows per chromHMM state, hg38.
- seqsetvis::chromHMM_demo_chain_urlURL to download hg19ToHg38 liftover chain from UCSC
- seqsetvis::chromHMM_demo_overlaps_groverlap of MCF10A CTCF with MCF7 chromHMM states, hg38.
- seqsetvis::chromHMM_demo_segmentation_urlURL to download hg19 MCF7 chromHMM segmentation
- seqsetvis::chromHMM_demo_state_colorsoriginal state name to color mappings stored in segmentation bed
- seqsetvis::chromHMM_demo_state_total_widthsstate name to total width mappings, hg38
- seqsetvis::test_peaks4 random peaks for single-end data and 4 control regions 30kb downstream from each peak.
- SeqVarTools::pedigreePedigree for example data
- SEtools::SEExample dataset
- sevenC::TFspecificModelsTF specific parameters for logistic regression in sevenC
- sevenC::cutoffBest10Default optimal cutoff value of logistic regression.
- sevenC::cutoffByTFOptimal cutoff values for logistic regression models.
- sevenC::modelBest10AvgDefault parameters for logistic regression model in sevenC.
- sevenC::motif.hg19.CTCFCTCF motif locations in human genome hg19.
- sevenC::motif.hg19.CTCF.chr22CTCF motif locations on chromosome 22 in human genome hg19.
- sevenC::motif.hg19.CTCF.chr22.covCTCF motifs on human chromosome 22 with example coverage.
- SGCP::chengNormalized gene expression data from Cheng et al.'s publication on ischemic cardiomyopathy (ICM).
- SGCP::resClusAn example of the output from 'clustering' function in the SGCP pipeline
- SGCP::resFinalGOAn example of the output from 'geneOntololgy' function in the SGCP pipeline
- SGCP::resInitialGOAn example of the output from the 'geneOntololgy' function in the SGCP pipeline
- SGCP::resSemiLabelAn example of the output from 'semiLabeling' function in the SGCP pipeline
- SGCP::resSemiSupervisedAn example of the output from 'semiSupervised' function in the SGCP pipeline
- SGCP::sgcpAn example of the output of 'ezSGCP' function in the SGCP pipeline
- SGSeq::grExample genomic region of interest
- SGSeq::sgf_annExample splice graph features (annotation-based)
- SGSeq::sgf_predExample splice graph features (predicted)
- SGSeq::sgfc_annExample splice graph feature counts (annotation-based)
- SGSeq::sgfc_predExample splice graph feature counts (predicted)
- SGSeq::sgv_annExample splice variants (annotation-based)
- SGSeq::sgv_predExample splice variants (predicted)
- SGSeq::sgvc_annExample splice variant counts (annotated)
- SGSeq::sgvc_ann_from_bamExample splice variant counts (annotated) from BAM files
- SGSeq::sgvc_predExample splice variant counts (predicted)
- SGSeq::sgvc_pred_from_bamExample splice variant counts (predicted) from BAM files
- SGSeq::siExample sample information
- SGSeq::txExample transcripts
- SGSeq::txf_annExample transcript features (annotation-based)
- SGSeq::txf_predExample transcript features (predicted)
- SIAMCAT::feat.crc.zellerExample feature matrix
- SIAMCAT::meta.crc.zellerExample metadata matrix
- SIAMCAT::siamcat_exampleSIAMCAT example
- SigCheck::classifyResultsPrecomputed list of results for a calls to 'sigCheckRandom' and 'sigCheckKnown' using the 'breastCancerNKI' dataset.
- SigCheck::knownSignaturesPreviously identified gene signatures for use in 'sigCheckKnown'
- SigCheck::nkiResultsPrecomputed list of results for a call to 'sigCheckAll' using the 'breastCancerNKI' dataset.
- sigFeature::ExampleRawDataExample dataset to test the performance of the sigFeature package.
- sigFeature::featsweepSigFeProcessed output data after using the function named "sigCVError()".
- sigFeature::featureRankedListProcessed output data after using the function named "svmrfeFeatureRanking()".
- sigFeature::resultsProcessed output data after using the function named "sigFeature.enfold()".
- sigFeature::sigfeatureRankedListProcessed output data after using the function named "sigFeature()".
- SigFuge::geneAnnotCDKN2A gene locus annotation
- SigFuge::geneDepthCoverage matrix across CDKN2A gene locus
- sights::ex_dataMatrixHigh-Throughput Screening example data - CMBA
- sights::ingleseHigh-Throughput Screening example data - Inglese
- signatureSearch::cell_infoLINCS 2017 Cell Type Information
- signatureSearch::cell_info2LINCS 2020 Cell Type Information
- signatureSearch::chembl_moa_listMOA to Gene Mappings
- signatureSearch::clue_moa_listMOA to Drug Name Mappings
- signatureSearch::drugs10Drug Names Used in Examples
- signatureSearch::lincs_expr_inst_infoInstance Information of LINCS Expression Database
- signatureSearch::lincs_pert_infoLINCS 2017 Perturbation Information
- signatureSearch::lincs_pert_info2LINCS 2020 Perturbation Information
- signatureSearch::lincs_sig_infoLINCS Signature Information
- signatureSearch::targetListTarget Sample Data Set
- signeR::cosmic_dataCOSMIC Mutational Signatures
- signeR::tcga_similaritiesTCGA Cosmic similarities
- signeR::tcga_tumorsTCGA tumors used on TCGA Explorer
- signifinder::ovseExample expression data.
- SigsPack::cosmicSigsCOSMIC Signature Profiles
- SigsPack::hg19context_freqTrinuecleotide frequencies of the human reference genome hg19
- SigsPack::sigProfiler20190522COSMIC v3 whole genome SBS Signature Profiles
- SigsPack::sigProfilerExomeCOSMIC v3 exome SBS Signature Profiles
- sigsquared::BrCa443Breast Cancer 443 Data Set
- SIM::acgh.dataArray Comparative Genomic Hybridization data
- SIM::chrom.tableTable with chromosome information
- SIM::expr.dataExpression data example
- SIM::samplesSamples for example data
- SIMAT::LibraryExtracted compound information from an MSL library.
- SIMAT::RItableExtracted RI standard information from a 'csv' file.
- SIMAT::RunExtracted peaks from one SIM run.
- SIMAT::TargetsTargets information in a list.
- SIMAT::target.tableExtracted target information from a 'csv' file.
- SIMD::EM2_H1ESB1_MeDIP_sigleCpGA simulation dataset of MeDIP CpG sites.
- SIMD::EM2_H1ESB2_MeDIP_sigleCpGA simulation dataset of MeDIP CpG sites.
- SIMD::EM_H1ESB1_MeDIP_sigleCpGA simulation dataset of MeDIP CpG sites.
- SIMD::H1ESB1_MRE_sigleCpGA simulation dataset of MRE CpG sites.
- SIMD::H1ESB2_MRE_sigleCpGA simulation dataset of MRE CpG sites.
- SIMD::all_CpGsite_bin_chr18A simulation dataset of CpG sites.
- SIMD::three_mre_cpgA simulation dataset of MRE CpG sites.
- similaRpeak::chr7ProfilesChIP-Seq profiles of region chr7:61968807-61969730 related to enhancers H3K27ac and H3K4me1 (for demonstration purpose)
- similaRpeak::demoProfilesChIP-Seq profiles of region chr7:61968807-61969730 related to enhancers H3K27ac and H3K4me1 (for demonstration purpose)
- SIMLR::BuettnerFloriantest dataset for SIMLR
- SIMLR::ZeiselAmittest dataset for SIMLR large scale
- sincell::ExpressionMatrixSingle-cell expression data for genes differentially expressed in differentiating human skeletal muscle myoblasts cells
- sincell::geneset.listExample of a geneset collection
- SingleCellSignalR::LRdbLigand/Receptor interactions data table
- SingleCellSignalR::PwC_ReactomeKEGGPathway Commons Reactome KEGG 2019-05-08
- SingleCellSignalR::example_datasetExample dataset
- SingleCellSignalR::markers_defaultA list of cell types markers
- SingleCellSignalR::mm2HsMus Musculus (mm) to Homo Sapiense (Hs) Orthology table
- singleCellTK::MitoGenesList of mitochondrial genes of multiple reference
- singleCellTK::SEGStably Expressed Gene (SEG) list obect, with SEG sets for human and mouse.
- singleCellTK::mouseBrainSubsetSCEExample Single Cell RNA-Seq data in SingleCellExperiment Object, GSE60361 subset
- singleCellTK::msigdb_tableMSigDB gene get Category table
- singleCellTK::sceExample Single Cell RNA-Seq data in SingleCellExperiment Object, subset of 10x public dataset
- singleCellTK::sceBatchesExample Single Cell RNA-Seq data in SingleCellExperiment object, with different batches annotated
- singscore::scoredf_ccle_epiPre-computed scores of the CCLE dataset against an epithelial gene signature
- singscore::scoredf_ccle_mesPre-computed scores of the CCLE dataset against a mesenchymal gene signature
- singscore::scoredf_tcga_epiPre-computed scores of the TCGA breast cancer gene expression matrix against an epithelial signature
- singscore::scoredf_tcga_mesPre-computed scores of the TCGA breast cancer gene expression matrix against a mesenchymal signature
- singscore::tgfb_expr_10_seAn example gene expression dataset
- singscore::tgfb_gs_dnGene set of down-regulated genes for the TGFb-induced EMT gene signature
- singscore::tgfb_gs_upGene set of up-regulated genes for the TGFb-induced EMT gene signature
- singscore::toy_expr_seA toy gene expression dataset of two samples
- singscore::toy_gs_dnA gene set object of down-regulated genes for the toy dataset
- singscore::toy_gs_upA gene set object of up-regulated genes for the toy dataset
- sitePath::h3n2_alignMultiple sequence alignment of H3N2's HA protein
- sitePath::h3n2_align_reducedMultiple sequence alignment of H3N2's HA protein
- sitePath::h3n2_treePhylogenetic tree of H3N2's HA protein
- sitePath::h3n2_tree_reducedPhylogenetic tree of H3N2's HA protein
- sitePath::sars2_alignMultiple sequence alignment of SARS-CoV-2 genome CDS
- sitePath::sars2_treePhylogenetic tree of SARS-CoV-2 genome CDS
- sitePath::zikv_alignMultiple sequence alignment of Zika virus polyprotein
- sitePath::zikv_align_reducedMultiple sequence alignment of Zika virus polyprotein
- sitePath::zikv_treePhylogenetic tree of Zika virus polyprotein
- sitePath::zikv_tree_reducedPhylogenetic tree of Zika virus polyprotein
- slalom::mescA single-cell expression dataset to demonstrate capabilities of slalom from mouse embryonic stem cells (mESCs)
- slingshot::slingshotExampleBifurcating lineages data
- SLqPCR::SLqPCRdataSIRS-Lab inhouse qPCR data
- SLqPCR::vandesompeleData set of Vandesompele et al (2002)
- SMAD::TestDatInputTest data for SMAD
- smartid::sim_sce_testscRNA-seq test data of 4 groups simulated by 'splatter'.
- SMITE::REACTOMEAn Igraph network for REACTOME with nodes as gene symbols
- SMITE::expression_curatedA toy dataset ofcurated RNA-seq to test within SMITE
- SMITE::genesA small set of RefSeq genes for converting
- SMITE::h3k4me1A toy dataset of H3k4me1 peaks to test within SMITE
- SMITE::hg19_genesA bed file annotating Refseq genes for the hg19 genome build
- SMITE::methylationA toy dataset of DNA methylation to test within SMITE
- SMITE::test_annotationA toy PvalueAnnotation
- SNPhood::SNPhood.oSNPhood example data
- SNPRelate::hapmap_genoSNP genotypes of HapMap samples
- snpStats::AsnpsTest data for the snpStats package
- snpStats::AutosomesTest data for the snpStats package
- snpStats::XchromosomeTest data for the snpStats package
- snpStats::XsnpsTest data for the snpStats package
- snpStats::ceph.1mbDatasets to illustrate calculation of linkage disequilibrium statistics
- snpStats::genotypesTest data for family association tests
- snpStats::pedDataTest data for family association tests
- snpStats::snp.supportData for exercise in use of the snpStats package
- snpStats::snps.10Data for exercise in use of the snpStats package
- snpStats::subject.dataTest data for the snpStats package
- snpStats::subject.supportData for exercise in use of the snpStats package
- snpStats::support.ldDatasets to illustrate calculation of linkage disequilibrium statistics
- snpStats::yri.1mbDatasets to illustrate calculation of linkage disequilibrium statistics
- soGGi::chipExampleBigExample ChIPprofiles
- soGGi::ik_ExampleExample Ikaros peaksets
- soGGi::ik_ProfilesExample Ikaros signal over peaksets
- soGGi::pwmCovExample motif coverage
- soGGi::singleGRangeA single GRange
- SomaticSignatures::k3weKmer datasets
- SomaticSignatures::k3wgKmer datasets
- SomaticSignatures::sca_mmSomaticCancerAlterations Results
- SomaticSignatures::sca_motifs_tinySomaticCancerAlterations Results
- SomaticSignatures::signatures2121 Signatures
- SomaticSignatures::sigs_nmfSomaticCancerAlterations Results
- SomaticSignatures::sigs_pcaSomaticCancerAlterations Results
- SOMNiBUS::RAdatMethylation data from a rheumatoid arthritis study
- SOMNiBUS::RAdat2A simulated methylation dataset based on a real data.
- SpaceMarkers::curated_genesCurated Genes for example purposes
- SpaceMarkers::optParamsOptimal paramters of 5 patterns from CoGAPS.
- sparsenetgls::bandprecbandprec data for vignette
- SparseSignatures::backgroundgermline replication error
- SparseSignatures::background2COSMIC replication error
- SparseSignatures::cv_exampleexample of results obtained with the function nmf.LassoCV on the counts input from Nik-Zainal, Serena, et al. (2016).
- SparseSignatures::imported_dataexample of imported data from Nik-Zainal, Serena, et al. (2016).
- SparseSignatures::lambda_range_exampleexample of results obtained with the function evaluate.lambda.range on the counts input from Nik-Zainal, Serena, et al. (2016).
- SparseSignatures::mutation_categoriestrinucleotides mutation categories
- SparseSignatures::nmf_LassoK_exampleexample of results obtained with the function nmf.LassoK on the counts input from Nik-Zainal, Serena, et al. (2016).
- SparseSignatures::patientspoint mutations for 560 breast tumors
- SparseSignatures::ssm560_reduceda reduced version of the point mutations for 560 breast tumors in the format compatible with the import function
- SparseSignatures::starting_betas_exampleexample of results obtained with the function starting.betas.estimation on the counts input from Nik-Zainal, Serena, et al. (2016).
- spaSim::bg1Background cells (4915 cells in a 2000*2000 window)
- spatialDE::MOB_sample_infoMouse Olfactory Bulb sample metadata
- spatialDE::Rep11_MOB_0Mouse Olfactory Bulb spatial gene expression data
- SpatialDecon::cellcolsDefault colors for the cell types in the safeTME matrix
- SpatialDecon::mean.resid.sdGenes' biological variability in immune deconvolution from TCGA.
- SpatialDecon::mini_geomx_datasetSmall example GeoMx data
- SpatialDecon::mini_singleCell_datasetMini human colon single cell dataset
- SpatialDecon::nsclcLarge example GeoMx data
- SpatialDecon::safeTMESafeTME matrix
- SpatialDecon::safeTME.matchesMapping from granularly-defined cell populations to broaded cell populations
- SpatialFeatureExperiment::visium_row_colRow and columns of Visium barcodes on the slide
- spatialHeatmap::aSVG.remote.repoA list of URLs of remote aSVG repos
- spatzie::anchor_pair_example_countspatzie count correlation data set
- spatzie::anchor_pair_example_matchspatzie match association data set
- spatzie::anchor_pair_example_scorespatzie score correlation data set
- spatzie::compare_pairs_examplecompare_motif_pairs example
- spatzie::filter_pairs_examplespatzie score correlation filtered data set
- spatzie::int_data_k562K562 Enhancer - Promoter Interactions Data Set
- spatzie::int_data_mslclMSLCL Enhancer - Promoter Interactions Data Set
- spatzie::int_data_yy1Mouse YY1 Enhancer - Promoter Interactions Data Set
- spatzie::interactions_yy1Mouse YY1 Enhancer - Promoter Interactions Data Set
- spatzie::interactions_yy1_enhancerMouse YY1 Enhancer - Promoter Interactions Data Set - YY1 enhancers
- spatzie::interactions_yy1_epMouse YY1 Enhancer - Promoter Interactions Data Set - YY1 enhancers/promoters
- spatzie::interactions_yy1_promoterMouse YY1 Enhancer - Promoter Interactions Data Set - YY1 promoters
- spatzie::scan_interactions_exampleInteractions scanned for motifs - interactionData object
- spatzie::scan_interactions_example_filteredInteractions with motifs filtered for significance - interactionData object
- speckle::pbmc_propsCell type proportions from single cell PBMC data
- specL::iRTpeptidesiRT peptides - independent retention time peptides
- specL::ms1.p2069ms1 mass
- specL::peptideStdPeptide standard
- specL::peptideStd.redundantPeptide standard
- SpeCond::expSetSpeCondExampleAn ExpressionSet example object used in the SpeCond package
- SpeCond::expressionSpeCondExampleThe expression matrix example used in the SpeCond package
- SpeCond::simulatedSpeCondDataAn example of simulated expression matrix used in the SpeCond package
- Spectra::fft_spectrumFast fourier transform artefact filter
- SpectralTAD::rao_chr20_25_repContact matrix from Rao 2014, chromosome 20, 25kb resolution
- SPEM::sosSOS pathway time series data
- SPIA::ALL_ColorectalResults from a microarray experiment comparing colorectal cancer samples and normal tissue samples.
- SPIA::ALL_VesselsResults from a microarray expriment comparing umbilical veins and arteries tissues
- SPIA::DE_ColorectalResults from a microarray experiment comparing colorectal cancer samples and normal tissue samples.
- SPIA::DE_VesselsResults from a microarray expriment comparing umbilical veins and arteries tissues
- SPIA::topResults from a microarray experiment comparing colorectal cancer samples and normal tissue samples.
- SPIAT::defined_imageSPE object of a simulated image with defined cell types based on marker combinations.
- SPIAT::image_no_markersSPE object of a formatted image without marker intensities (simulated by 'spaSim' package)
- SPIAT::simulated_imageSPE object of a formatted image (simulated by 'spaSim' package)
- spicyR::diabetesDataDiabetes IMC data in SCE format.
- spicyR::spicyTestResults from spicy for diabetesData
- spikeLI::SPIKE_INSpike-in Probe-Set Names
- spikeLI::SPIKE_IN95set of spike-in genes contained in the HGU95 dataset
- spikeLI::SPIKE_INAArtificial Spike-in probesets
- spikeLI::SPIKE_INBBacteria Spike-in probeset names
- spikeLI::SPIKE_INHHuman Spike-in probe-set names
- spikeLI::conc133Concentration 95
- spikeLI::conc95Concentration 95
- spikeLI::hguSelected Probe Set data
- spiky::dedupspike-in counts for two samples, as a wide data.frame
- spiky::genbank_mitovarious mitochondrial genomes sometimes used as endogenous spike-ins
- spiky::genomic_resA Granges object with genomic coverage from chr21q22, binned every 300bp for the genomic contigs then averaged across the bin. (In other words, the default output of scan_genomic_contigs or scan_genomic_bedpe, restricted to a small enough set of genomic regions to be practical for examples.) This represents what most users will want to generate from their own genomic BAMs or BEDPEs, and is used repeatedly in downstream examples throughout the package.
- spiky::phagelambda and phiX phage sequences, sometimes used as spike-ins
- spiky::spikespike-in contig properties for Sam's cfMeDIP spikes
- spiky::spike_cram_countsspike-in counts, as a long data.frame
- spiky::spike_read_countsspike-in counts, as a long data.frame
- spiky::spike_resA Granges object with spike-in sequence coverage, and summarized for each spike contig as (the default) 'max' coverage. (In other words, the default output of scan_spike_contigs or scan_spike_bedpe) This represents what most users will want to generate from their own spike-in BAMs or BEDPEs, and is used repeatedly in downstream examples throughout the package.
- spiky::ssb_resscan_spiked_bam results from a merged cfMeDIP CRAM file (chr22 and spikes)
- spiky::testGRa test GRanges with UMI'ed genomic sequences used as controls
- spkTools::affySpikeInExpressionSet of Affymetrix Spike-in Experiment Data
- SplicingFactory::tcga_brca_luma_datasetTCGA Luminal A breast cancer dataset
- splineTimeR::TCsimDataSimulated time-course gene expression data set
- SPLINTER::acceptor.macceptor.m
- SPLINTER::compatible_cdscompatible_cds
- SPLINTER::compatible_txcompatible_tx
- SPLINTER::donor.mdonor.m
- SPLINTER::pcr_result1pcr_result1
- SPLINTER::primersprimers
- SPLINTER::region_minus_exonregion_minus_exon
- SPLINTER::roiroi
- SPLINTER::splice_datasplice_data
- SPLINTER::splice_fastasplice_fasta
- SPLINTER::thecdsthecds
- SPLINTER::theexonstheexons
- SPLINTER::valid_cdsvalid_cds
- SPLINTER::valid_txvalid_tx
- SPONGE::ceRNA_interactionsceRNA interactions
- SPONGE::ensembl.dfexample potential central nodes
- SPONGE::gene_exprGene expression test data set
- SPONGE::mir_exprmiRNA expression test data set
- SPONGE::mir_interactionsmiRNA / gene interactions
- SPONGE::mircode_ensgmircode predicted miRNA gene interactions
- SPONGE::mircode_symbolmircode predicted miRNA gene interactions
- SPONGE::precomputed_cov_matricescovariance matrices under the null hypothesis that sensitivity correlation is zero
- SPONGE::precomputed_null_modelA null model for testing purposes
- SPONGE::targetscan_ensgtargetscan predicted miRNA gene interactions
- SPONGE::targetscan_symboltargetscan predicted miRNA gene interactions
- SPONGE::test_cancer_gene_exprexample test expression data for spongEffects
- SPONGE::test_cancer_metadataexample test sample meta data for spongEffects
- SPONGE::test_cancer_mir_exprexample test miRNA data for spongEffects
- SPONGE::train_cancer_gene_exprexample training expression data for spongEffects
- SPONGE::train_cancer_metadataexample training sample meta data for spongEffects
- SPONGE::train_cancer_mir_exprexample training miRNA data for spongEffects
- SPONGE::train_ceRNA_interactionsexample train ceRNA interactions for spongEffects
- SPONGE::train_genes_miRNA_candidates
- SPONGE::train_network_centralitiesexample train network centralities for spongEffects
- SpotClean::mbrain_rawExample 10x Visium spatial data: raw count matrix
- SpotSweeper::DLPFC_artifacthuman DLPFC dataset with a technical artifact (hangnail).
- SPsimSeq::scNGP.dataNeuroblastoma NGP cells single-cell RNA-seq.
- SPsimSeq::zhang.data.subNeuroblastoma bulk RNA-seq data retrieved from Zhang et (2015).
- sRACIPE::CoupledToggleSwitchSAFive coupled toggle switches
- sRACIPE::EMT1A circuit for epithelial to mesenchymal transition
- sRACIPE::EMT2A circuit for epithelial to mesenchymal transition including microRNAs
- sRACIPE::configDataConfiguration Data
- sRACIPE::demoCircuitA toggle switch circuit for demonstrations
- sSeq::countsTableAn Example Simulation Data
- sSeq::countsTableAn Example Simulation Data
- sSeq::countsTableAn Example Simulation Data
- sSeq::countsTableAn Example Simulation Data
- ssize::exp.sdExample baseline variability for gene expression experiment
- sSNAPPY::gsAnnotation_dfgsAnnotation_df: Categorization of KEGG pathways used for community annotation
- sSNAPPY::logCPM_examplelogCPM_example: Normalised logCPM of patient-derived explant models obtained from 5 ER-positive primamry breast cancer tumours (GSE80098)
- sSNAPPY::metadata_examplemetadata_example: Sample metadata for malignant breast cancer tumours PDE from 5 ER+ breast cancer tumour (GSE80098)
- ssPATHS::expected_score_outputGene Expression Values for PDAC Cancer Cell Lines exposed to Hypoxia
- ssPATHS::gene_weights_referenceGene Expression Values for PDAC Cancer Cell Lines exposed to Hypoxia
- ssPATHS::new_samp_dfGene Expression Values for PDAC Cancer Cell Lines exposed to Hypoxia
- ssPATHS::tcga_expr_dfGene Expression Values for PDAC Cancer Cell Lines exposed to Hypoxia
- ssrch::docset_cancer68DocSet instance with metadata from 68 cancer studies
- ssrch::study_publ_datespublication dates for 6000 SRA transcriptome studies
- ssrch::titles68titles for 68 cancer studies
- ssrch::urls68pubmed URLs for subset of 68 cancer studies
- ssviz::countscounts data
- ssviz::ctrlbamctrlbam data
- ssviz::pctrlbampctrlbam data
- ssviz::ptreatbamptreatbam data
- ssviz::treatbamtreatbam data
- stageR::esetProstateTranscript-level abundance estimates in 14 Chinese prostate cancer patients
- stageR::hammer.esetHammer dataset
- standR::dkd_spe_subsetDescription of the standR example datasets
- STATegRa::Block1STATegRa data
- STATegRa::Block1.PCASTATegRa data
- STATegRa::Block2STATegRa data
- STATegRa::Block2.PCASTATegRa data
- STATegRa::TCGA_BRCA_DataSTATegRa data
- STATegRa::edSTATegRa data
- STATegRa::ed.PCASTATegRa data
- STATegRa::mapdataSTATegRa data
- Statial::kerenKontextualKontextual results from kerenSCE
- Statial::kerenSCEMIBI-TOF Breast cancer intensities
- STdeconvolve::mOBSpatial transcriptomics of the mouse olfactory bulb
- STRINGdb::diff_exp_example1example of microarray data (data processed from GEO GSE9008)
- STRINGdb::interactions_exampleexample of a protein-protein interactions sorted data frame
- Structstrings::dbsStructstrings example data
- Structstrings::nseqStructstrings example data
- SubCellBarCode::hcc827CtrlHCC827 Control Cell Line
- SubCellBarCode::hcc827CtrlPSMCountMinimum PSM Count in HCC827Ctrl Cell Line.
- SubCellBarCode::hcc827GEFGefitinib treated HCC827 Cell Line
- SubCellBarCode::hcc827GEFClassGefitinib treated HCC827 Cell Line Classification
- SubCellBarCode::hcc827GefPSMCountMinimum PSM Count in HCC827 Gefitinib Cell Line.
- SubCellBarCode::hcc827exonHCC827 Control Exon Cell Line
- SubCellBarCode::markerProteinsMarker Proteins Source
- subSeq::hammerExpressionSet results from Hammer et al 2010
- subSeq::ssSubsampling results using the hammer dataset
- SUITOR::SimDataData for examples
- SUITOR::plotDataExample data for plotting
- SUITOR::resultssuitor return object
- Summix::ancestryDataancestryData
- supersigs::example_dtExample dataset of mutations
- supersigs::supersig_lsTrained SuperSigs from TCGA
- supraHex::FangHuman embryo gene expression dataset from Fang et al. (2010)
- supraHex::Fang.geneinfoHuman embryo gene expression dataset from Fang et al. (2010)
- supraHex::Fang.sampleinfoHuman embryo gene expression dataset from Fang et al. (2010)
- supraHex::GolubLeukemia gene expression dataset from Golub et al. (1999)
- supraHex::XiangArabidopsis embryo gene expression dataset from Xiang et al. (2011)
- SurfR::countDatacountData
- SurfR::enrichedListenrichedList
- SurfR::ind_degind_deg
- SurfR::metadatametadata
- survClust::simdatSimulated dataset with 3-class solution
- survClust::simsurvdatSimulated survival dataset with accompanying 'simdat'
- survClust::uvm_datTCGA UVM Mutation and Copy Number datasets
- survClust::uvm_survClust_cv.fitsurvClust cv.survclust output of integrated TCGA UVM Mutation and Copy Number datasets.
- survClust::uvm_survdatTCGA UVM Clinical file
- survcomp::mainz7gSubset of MAINZ dataset containing gene expression, annotations and clinical data.
- survcomp::nki7gSubset of NKI dataset containing gene expression, annotations and clinical data.
- survcomp::transbig7gSubset of the TRANSBIG dataset containing gene expression, annotations and clinical data.
- survcomp::unt7gSubset of UNT dataset containing gene expression, annotations and clinical data.
- survcomp::upp7gSubset of UPP dataset containing gene expression, annotations and clinical data.
- survcomp::vdx7gSubset of VDX dataset containing gene expression, annotations and clinical data.
- SWATH2stats::MSstats_dataTesting dataset in MSstats format.
- SWATH2stats::OpenSWATH_dataTesting dataset from OpenSWATH.
- SWATH2stats::Study_designA table containing the meta-data defining the study design of the OpenSWATH data.
- SWATH2stats::dataTesting dataset from OpenSWATH.
- swfdr::BMI_GIANT_GWAS_sampleSubset of SNPs from meta-analysis of BMI GWAS study.
- swfdr::journals_pValsP-values from abstracts from articles in 5 biomedical journals (American Journal of Epidemiology, BMJ, JAMA, Lancet, New England Journal of Medicine), over 11 years (2000-2010).
- switchBox::matTestingGene expression matrix for test set data
- switchBox::matTrainingGene expression matrix for training set data
- switchBox::testingGroupTesting set phenotypes
- switchBox::trainingGroupTraining set phenotypes
- switchde::ex_pseudotimeSynthetic gene pseudotimes
- switchde::synth_gexSynthetic gene expression matrix
- synapter::synapterTinyLoads a small test data for the 'synapter' package
- synergyfinder::NCATS_screening_dataA high-throughput 3 drug combination screening data
- synergyfinder::ONEIL_screening_dataA high-throughput 2 drugs combination screening data with replication
- synergyfinder::mathews_screening_dataA high-throughput drug combination screening data
- SynExtend::BuiltInEnsemblesPretrained EvoWeaver Ensemble Models
- SynExtend::CIDist_NullDistSimulated Null Distributions for CI Distance
- SynExtend::Endosymbionts_GeneCallsExample genecalls
- SynExtend::Endosymbionts_LinkedFeaturesExample synteny links
- SynExtend::Endosymbionts_Pairs01Example predicted pairs
- SynExtend::Endosymbionts_Pairs02Example predicted pairs
- SynExtend::Endosymbionts_Pairs03Example predicted pairs
- SynExtend::Endosymbionts_SetsA list of disjoint sets.
- SynExtend::Endosymbionts_SyntenyA synteny object
- SynExtend::ExampleStreptomycesDataExample EvoWeaver Input Data from _Streptomyces_ Species
- SynExtend::GenericModel for predicting PID based on k-mer statistics
- SynExtend::SuperTreeExExample Dendrograms
- synlet::example_dtSynthetic lethal RNAi screen example data.
- syntenet::angiosperm_phylogenyMicrosynteny-based angiosperm phylogeny.
- syntenet::annotationFiltered genome annotation for Ostreococcus sp. species
- syntenet::blast_listList of data frames containing BLAST-like tabular output
- syntenet::clustersSynteny network clusters of BUSCO genes for 25 eudicot species
- syntenet::edgesSynteny network of Ostreococcus genomes represented as an edge list
- syntenet::networkSynteny network of BUSCO genes for 25 eudicot species
- syntenet::proteomesFiltered proteomes of Ostreococcus sp. species
- syntenet::scerevisiae_annotGenome annotation of the yeast species S. cerevisiae
- syntenet::scerevisiae_diamondIntraspecies DIAMOND output for S. cerevisiae
- tadar::chr1_genesGenomic feature example data
- TADCompare::GM12878.40kb.raw.chr2A subset of chomosome 2 contact matrix, GM12878 cell line.
- TADCompare::IMR90.40kb.raw.chr2A subset of chomosome 2 contact matrix, IMR90 cell line.
- TADCompare::rao_chr22_primChromosome 22 combined intrachromosomal primary contact matrix from Rao et al. 2014.
- TADCompare::rao_chr22_repChromosome 22 combined intrachromosomal replicate contact matrix from Rao et al. 2014.
- TADCompare::time_matsChromosome 22 time-varying contact matrices from Rao et al. 2017.
- TAPseq::bone_marrow_genexMouse bone marrow 10x data
- TAPseq::chr11_genesChromosome 11 genes
- TAPseq::chr11_polyA_sitesChromosome 11 polyA sites
- TAPseq::chr11_primersChromosome 11 primers
- TAPseq::chr11_truncated_txsChromosome 11 truncated transcripts
- TAPseq::chr11_truncated_txs_seqChromosome 11 truncated transcript sequences
- target::real_peaksAR peaks in LNCaP cell line
- target::real_transcriptsDifferential expression of DHT treated LNCaP cell line
- target::sim_peaksSimulated peaks
- target::sim_transcriptsSimulated transcripts The transcripts chromosome 1 of the mm10 mouse genome with randomly singed statistics assigned to each.
- TargetDecoy::ModSwissSwiss-Prot MS-GF+ data
- TargetDecoy::ModSwissXTSwiss-Prot X!Tandem data
- TargetSearch::RImatrixExample GC-MS data for TargetSearch Package
- TargetSearch::corRIExample GC-MS data for TargetSearch Package
- TargetSearch::metabProfileExample GC-MS data for TargetSearch Package
- TargetSearch::peakDataExample GC-MS data for TargetSearch Package
- TargetSearch::refLibraryExample GC-MS data for TargetSearch Package
- TargetSearch::rimLimitsClass for representing retention index markers
- TargetSearch::sampleDescriptionExample GC-MS data for TargetSearch Package
- TBSignatureProfiler::COVIDsignaturesA list of published/pre-print COVID-19 signatures.
- TBSignatureProfiler::OriginalTrainingDataDiscovery datasets for corresponding gene signatures.
- TBSignatureProfiler::TB_hivAn example TB dataset with TB/HIV data.
- TBSignatureProfiler::TB_indianAn example TB dataset with Indian population data.
- TBSignatureProfiler::TBcommonA list of published TB signatures, using author-given names.
- TBSignatureProfiler::TBsignaturesA list of published TB signatures.
- TBSignatureProfiler::TBsignaturesSplitUp/Down-regulated genes information for selected TB signatures.
- TBSignatureProfiler::common_sigAnnotDataAnnotation information for published TB signatures.
- TBSignatureProfiler::sigAnnotDataAnnotation information for published TB signatures.
- TCC::arabArabidopsis RNA-Seq data set
- TCC::hypoDataA simulation dataset for comparing two-group tag count data, focusing on RNA-seq
- TCC::hypoData_mgA simulation dataset for comparing three-group tag count data, focusing on RNA-seq
- TCC::hypoData_tsA sample microarray data for detecting tissue-specific patterns.
- TCC::nakaiDNA microarray data set
- TCGAbiolinks::DE_PCBC_stemSigA numeric vector with SC-derived definitive endoderm (DE) signature trained on PCBC's dataset
- TCGAbiolinks::EB_PCBC_stemSigA numeric vector with stem cell (SC)-derived embryoid bodies (EB) signature trained on PCBC's dataset
- TCGAbiolinks::ECTO_PCBC_stemSigA numeric vector with SC-derived ectoderm (ECTO) signature trained on PCBC's dataset
- TCGAbiolinks::MESO_PCBC_stemSigA numeric vector with SC-derived mesoderm (MESO) signature trained on PCBC's dataset
- TCGAbiolinks::SC_PCBC_stemSigA numeric vector with stem cell-like signature trained on PCBC's dataset
- TCGAbiolinks::TabSubtypesCol_mergedTCGA samples with their Pam50 subtypes
- TCGAbiolinks::Tumor.purityTCGA samples with their Tumor Purity measures
- TCGAbiolinks::bcgsc.ca_CHOL.IlluminaHiSeq_DNASeq.1.somatic.mafTCGA CHOL MAF
- TCGAbiolinks::chol_mafTCGA CHOL MAF transformed to maftools object
- TCGAbiolinks::clinical.biotabA list of data frames with clinical data parsed from XML (code in vignettes)
- TCGAbiolinks::dataBRCATCGA data matrix BRCA
- TCGAbiolinks::dataDEGsFiltLevelTCGA data matrix BRCA DEGs
- TCGAbiolinks::dataREADTCGA data SummarizedExperiment READ
- TCGAbiolinks::dataREAD_dfTCGA data matrix READ
- TCGAbiolinks::gbm.exp.harmonizedA RangedSummarizedExperiment two samples with gene expression data from vignette aligned against hg38
- TCGAbiolinks::gbm.exp.legacyA RangedSummarizedExperiment two samples with gene expression data from vignette aligned against hg19
- TCGAbiolinks::geneInfogeneInfo for normalization of RNAseq data
- TCGAbiolinks::geneInfoHTgeneInfoHT for normalization of HTseq data
- TCGAbiolinks::met.gbm.27kA DNA methylation RangedSummarizedExperiment for 8 samples (only first 20 probes) aligned against hg19
- TCGAbiolinks::msi_resultsMSI data for two samples
- TCGAbiolinks::tabSurvKMcompleteDEGstabSurvKMcompleteDEGs
- TCGAutils::clinicalNamesClinical dataset names in TCGA
- TCGAutils::diseaseCodesTCGA Cancer Disease Codes Table
- TCGAutils::sampleTypesBarcode Sample Type Table
- TCseq::countsTableAn example read Counts table
- TCseq::experimentAn example experiment design without BAM file infomration
- TCseq::experiment_BAMfileAn example experiment design with BAM file infomration
- TCseq::genomicIntervalsAn example reference genomic regions
- TCseq::tca_ATACAn example TCA object
- TEKRABber::ctInputDEInput expression data of gene/TE for differentially expressed analysis within same species
- TEKRABber::fetchDataHmChimpExample output comparing human and chimpanzee data using orhtologScale()
- TEKRABber::hg38_panTro6_rmskRepeatmasker track annotations with human and chimpanzee
- TEKRABber::speciesCountsGene/TE expression data from human/chimpanzee brain RNA-seq
- TFARM::DELTAContains the delta variations of support, confidence and lift.
- TFARM::IMPContains the mean Importance Index of each co-regulator.
- TFARM::IMP_ZContains the Importance Index associated with each co-regulator which is present in at least one association rule.
- TFARM::I_c_2Contains the mean Importance Index of pairs of transcription factors which are present in at least one association rule.
- TFARM::MCF7_chr1Contains genomic regions in the first chromosome of the MCF-7 human breast adenocarcinoma cell line at the ranges side, and the presence indexes of transcription factors in such regions at the metadata side.
- TFARM::TF_ImpContains the candidate co-regulators and the number of rules associated with them.
- TFARM::imp_FOSL2Contains the set of Importance Indexes of FOSL2 in a given set of rules.
- TFARM::p_TFsContains co-regulators found in at least one association rule.
- TFARM::r_FOSL2Represents an example of rulesTF output, i.e. the subset of rules whose left-hand-sides contain FOSL2, and the correspondent quality measures.
- TFARM::r_TEAD4Contains the association rules for the prediction of the presence of the transcription factor TEAD4 in the considered genomic regions, i.e., with TEAD4 in the right-hand-side of the association rules.
- TFARM::r_noFOSL2Represents an example of rulesTF0 output, where the presence of FOSL2 was replaced with its absence.
- TFBSTools::MA0003.2Some example PFM matrices.
- TFBSTools::MA0004.1Some example PFM matrices.
- TFBSTools::MA0043Some example PFM matrices.
- TFBSTools::MA0048Some example PFM matrices.
- TFEA.ChIP::ARNT.metadataMetadata data frame
- TFEA.ChIP::ARNT.peaks.bedChIP-Seq dataset
- TFEA.ChIP::ChIPDBTF-gene binding binary matrix
- TFEA.ChIP::DnaseHS_dbDHS databse
- TFEA.ChIP::Entrez.gene.IDsList of Entrez Gene IDs
- TFEA.ChIP::GSEA.resultOutput of the function GSEA.run from the TFEA.ChIP package
- TFEA.ChIP::Genes.UpregList of Entrez Gene IDs
- TFEA.ChIP::MetaDataTF-gene binding DB metadata
- TFEA.ChIP::gr.listList of one ChIP-Seq dataset
- TFEA.ChIP::hypoxiaRNA-Seq experiment
- TFEA.ChIP::hypoxia_DESeqRNA-Seq experiment
- TFEA.ChIP::log2.FCList of Entrez Gene IDs
- TFHAZ::IshikawaContains genomic regions of transcription factors at the ranges side and the name of the transcription factors at the metadata side.
- TFHAZ::TF_acc_w_0Contains an output of the accumulation function.
- TFHAZ::TF_dense_w_0Contains an output of the dense_zones function.
- TFHAZ::TF_dense_w_10Contains an output of the dense_zones function.
- TFHAZ::TF_dense_w_100Contains an output of the dense_zones function.
- TFHAZ::TF_dense_w_1000Contains an output of the dense_zones function.
- TFHAZ::TF_dense_w_10000Contains an output of the dense_zones function.
- TFHAZ::base_dense_w_10Contains an output of the dense_zones function.
- TFHAZ::reg_dense_w_10Contains an output of the dense_zones function.
- TFutils::cisbpTFcatcisbpTFcat: data.frame with information on CISBP TFs for human, retained for reproducibility support; see cisbpTFcat_2.0 for a more recent catalog
- TFutils::cisbpTFcat_2.0cisbpTFcat_2.0: data.frame with information on CISBP TFs for human, described in PMID 31133749
- TFutils::demo_fimo_grangesa list of GRanges instances with TF FIMO scores returned by 'fimo_granges'
- TFutils::encode690encode690: DataFrame extending AnnotationHub metadata about ENCODE cell line x TF ranges
- TFutils::fimo16fimo16: GenomicFiles instance to AWS S3-resident FIMO bed for 16 TFs
- TFutils::fimoMapfimoMap: table with Mnnnn (motif PWM tags) and HGNC symbols for TFs
- TFutils::gwascat_hg19_chr17gwascat_hg19: GRanges of march 21 2018 EBI gwascat, limit to chr17
- TFutils::hocomoco.monohocomoco.mono: data.frame with information on HOCOMOCO TFs for human
- TFutils::hocomoco.mono.sep2018hocomoco.mono.sep2018: data.frame with information on HOCOMOCO TFs for human, Sept 2018 download
- TFutils::lambert_snpslambert_snps is Table S3 of Lambert et al PMID 29425488
- TFutils::metadata_tfmetadata_tf: list with metadata (motif_if and hgnc_symbol) about all the CISBP FIMO scan TF bed files
- TFutils::named_tfnamed_tf: named list with the names being the hgnc_symbol of the motif_id
- TFutils::seqinfo_hg19_chr17a Seqinfo instance for a chr17 in hg19
- TFutils::tfhashtfhash: data.frame with MSigDb TFs, TF targets as symbol or ENTREZ
- TFutils::tftColltftColl: GSEABase GeneSetCollection for transcription factor targets
- TFutils::tftCollMaptftCollMap: data.frame with information on MSigDb TFs for human
- tidybulk::X_cibersortCibersort reference
- tidybulk::breast_tcga_mini_SENeeded for vignette breast_tcga_mini_SE
- tidybulk::counts_ensemblCounts with ensembl annotation
- tidybulk::ensembl_symbol_mappingData set
- tidybulk::flybaseIDsflybaseIDs
- tidybulk::seSummarizedExperiment
- tidybulk::se_miniSummarizedExperiment mini for vignette
- tidybulk::tximeta_summarizeToGene_objectNeeded for tests tximeta_summarizeToGene_object, It is SummarizedExperiment from tximeta
- tidybulk::vignette_manuscript_signature_boxplotNeeded for vignette vignette_manuscript_signature_boxplot
- tidybulk::vignette_manuscript_signature_tsneNeeded for vignette vignette_manuscript_signature_tsne
- tidybulk::vignette_manuscript_signature_tsne2Needed for vignette vignette_manuscript_signature_tsne2
- tidyCoverage::acExample 'CoverageExperiment' and 'AggregatedCoverage' objects
- tidyCoverage::ceExample 'CoverageExperiment' and 'AggregatedCoverage' objects
- tidyFlowCore::metal_masterlistA character vector of CyTOF metal name patterns supported by tidyFlowCore
- tidySingleCellExperiment::cell_type_dfCell types of 80 PBMC single cells
- tidySingleCellExperiment::pbmc_smallpbmc_small
- tidySingleCellExperiment::pbmc_small_nested_interactionsIntercellular ligand-receptor interactions for 38 ligands from a single cell RNA-seq cluster.
- tidySpatialExperiment::demo_brush_dataDemo brush data
- tidySpatialExperiment::demo_select_dataDemo select data
- tidySummarizedExperiment::pasillaRead counts of RNA-seq samples of Pasilla knock-down by Brooks et al.
- tidySummarizedExperiment::seRead counts of RNA-seq samples derived from Pasilla knock-down by Brooks et al.
- tidytof::ddpr_dataCyTOF data from two samples: 5,000 B-cell lineage cells from a healthy patient and 5,000 B-cell lineage cells from a B-cell precursor Acute Lymphoblastic Leukemia (BCP-ALL) patient.
- tidytof::ddpr_metadataClinical metadata for each patient sample in Good & Sarno et al. (2018).
- tidytof::metal_masterlistA character vector of metal name patterns supported by tidytof.
- tidytof::phenograph_dataCyTOF data from 6,000 healthy immune cells from a single patient.
- tigre::drosophila_gpsim_fragmentFragment of 12 time point Drosophila embryonic development microarray gene expression time series
- tigre::drosophila_mmgmos_fragmentFragment of 12 time point Drosophila embryonic development microarray gene expression time series
- tilingArray::gffSubExample of a genomic feature object
- tilingArray::segnfExample of a segmentation output object
- timecourse::fruitflyDrosophila microarray time course data in Tomancak et al. (2002)
- timeOmics::timeOmics.simdata
- TIN::geneAnnotationgeneAnnotation
- TIN::geneSetsgeneSets
- TIN::sampleSetFirmaScoressampleSetFirmaScores
- TIN::sampleSetGeneSummariessampleSetGeneSummaries
- TIN::splicingFactorsA list of 280 splicing factor genes
- TitanCNA::convergeParamsTITAN EM trained results for an example dataset
- TitanCNA::dataTITAN EM trained results for an example dataset
- tLOH::humanGBMsampleACImported dataset of a human glioblastoma spatial transcriptomics sample processed with tLOHImportData.
- tLOH::initialStartProbabilitiesImported dataset of sample start probabilities for hiddenMarkovAnalysis
- TMixClust::best_clust_toy_objTMixClust object containing the optimal clustering solution for the toy data with 3 clusters.
- TMixClust::best_clust_yeast_objTMixClust object containing the optimal clustering solution for the yeast data.
- TMixClust::toy_data_dfSimulated time-series gene expression data
- TOAST::CBS_PBMC_arrayAn example dataset for partial reference-free cell composition estimation from tissue gene expression
- TOAST::RA_100samplesAn example dataset for cellular proportion estimation and multiple factor design
- TOAST::beta_empSimulated methylation 450K array data with related
- tomoda::zh.dataA raw read count matrix of zebrafish injured heart.
- tomoseqr::maskA matrix containing mask data.
- tomoseqr::testxA data.frame object containing a simulated Tomo-seq data for x-axis sections.
- tomoseqr::testyA data.frame object containing a simulated Tomo-seq data for y-axis sections.
- tomoseqr::testzA data.frame object containing a simulated Tomo-seq data for z-axis sections.
- tomoseqr::tomoObjA tomoSeq object.
- TOP::TOP_data_binaryA simulated binary data
- topdownr::tdsTopDownSet Example Data
- topGO::GOdataSample topGOdata and topGOresult objects
- topGO::affyLibA toy example of a list of gene identifiers and the respective p-values
- topGO::geneListA toy example of a list of gene identifiers and the respective p-values
- topGO::resultFisherSample topGOdata and topGOresult objects
- topGO::resultKSSample topGOdata and topGOresult objects
- topGO::topDiffGenesA toy example of a list of gene identifiers and the respective p-values
- ToxicoGx::HCC_sigHCC_sig dataset
- ToxicoGx::TGGATESsmallTGGATESsmall dataset
- TPP::hdacCCR_configThe configuration table to analyze hdacCCR_data.
- TPP::hdacCCR_dataTPP-CCR example dataset (replicates 1 and 2)
- TPP::hdacTR_configThe configuration table to analyze hdacTR_data.
- TPP::hdacTR_dataTPP-TR example dataset.
- TPP::panobinostat_2DTPP_configThe configuration table to analyze panobinostat_2DTPP_data.
- TPP::panobinostat_2DTPP_data2D-TPP-CCR example dataset
- TPP::resultTableExample of a TPP-TR result table.
- TPP::tppRefDataExample of a reference dataset for 2D-TPP experiments.
- TPP2D::config_tabExample config table for a import of a simulated 2D-TPP cell extract dataset
- TPP2D::raw_dat_listExample raw data for a subset of a simulated 2D-TPP cell extract dataset
- TPP2D::simulated_cell_extract_dfExample subset of a simulated 2D-TPP cell extract dataset
- tracktables::IntervalsExample genomic intervals
- tradeSeq::celltypeA vector defining cell types, used in the package vignette.
- tradeSeq::countMatrixA count matrix, used in the package vignette.
- tradeSeq::crvA SlingshotDataset object, used in the package vignette.
- tradeSeq::gamListA list of GAM models, used to demonstrate the various tests.
- tradeSeq::sdsA SlingshotDataset object, used in the package unit tests.
- TrajectoryGeometry::chol_answerschol_answers
- TrajectoryGeometry::chol_attributeschol_attributes
- TrajectoryGeometry::chol_branch_point_resultschol_branch_point_results
- TrajectoryGeometry::chol_pseudo_timechol_pseudo_time
- TrajectoryGeometry::chol_pseudo_time_normalisedchol_pseudo_time_normalised
- TrajectoryGeometry::crooked_pathCrooked path
- TrajectoryGeometry::crooked_path_centerCrooked path center
- TrajectoryGeometry::crooked_path_projectionCrooked path projection
- TrajectoryGeometry::crooked_path_radiusCrooked path radius
- TrajectoryGeometry::hep_answershep_answers
- TrajectoryGeometry::hep_attributeshep_attributes
- TrajectoryGeometry::hep_pseudo_timehep_pseudo_time
- TrajectoryGeometry::hep_pseudo_time_normalisedhep_pseudo_time_normalised
- TrajectoryGeometry::oscillationOscillation
- TrajectoryGeometry::single_cell_matrixsingle_cell_matrix
- TrajectoryGeometry::straight_pathStraight path
- TrajectoryGeometry::straight_path_centerStraight path center
- TrajectoryGeometry::straight_path_projectionStraight path projection
- TrajectoryGeometry::straight_path_radiusStraight path radius
- transcriptogramer::DEsymbolsDictionary Protein2Symbol
- transcriptogramer::GPL570Dictionary Protein2Probe
- transcriptogramer::GSE9988Dataset containing expression values
- transcriptogramer::Hs700Ordered Homo sapiens proteins of combined score greater than or equal to 700
- transcriptogramer::Hs800Ordered Homo sapiens proteins of combined score greater than or equal to 800
- transcriptogramer::Hs900Ordered Homo sapiens proteins of combined score greater than or equal to 900
- transcriptogramer::HsBPTermsDictionary Protein2GO
- transcriptogramer::Mm700Ordered Mus musculus proteins of combined score greater than or equal to 700
- transcriptogramer::Mm800Ordered Mus musculus proteins of combined score greater than or equal to 800
- transcriptogramer::Mm900Ordered Mus musculus proteins of combined score greater than or equal to 900
- transcriptogramer::Rn700Ordered Rattus norvegicus proteins of combined score greater than or equal to 700
- transcriptogramer::Rn800Ordered Rattus norvegicus proteins of combined score greater than or equal to 800
- transcriptogramer::Rn900Ordered Rattus norvegicus proteins of combined score greater than or equal to 900
- transcriptogramer::Sc700Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 700
- transcriptogramer::Sc800Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 800
- transcriptogramer::Sc900Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 900
- transcriptogramer::associationAssociation
- transcriptR::annotReference annotation (knownGene from UCSC)
- transcriptR::cdsExample of 'ChipDataSet' object.
- transcriptR::tdsExample of 'TranscriptionDataSet' object.
- transite::geToy Gene Expression Data Set
- transite::kmers_enrichmentExample _k_-mer Enrichment Data
- transite::motifsTransite Motif Database
- transite::toy_motif_matrixToy Motif Matrix
- tRanslatome::CCComparisonSample data set for tRanslatome
- tRanslatome::CCEnrichmentSample data set for tRanslatome
- tRanslatome::expressionMatrixSample data set for tRanslatome
- tRanslatome::limma.DEGsSample data set for tRanslatome
- tRanslatome::regulatory.elements.countsSample data set for tRanslatome
- tRanslatome::regulatory.elements.regulatedSample data set for tRanslatome
- tRanslatome::translatome.analysisSample data set for tRanslatome
- traseR::CEUSampled SNPs from all SNPs of CEU population in 1000 genome project
- traseR::TcellPeak regions of H3K4me1 in Peripheral blood T cell
- traseR::taSNPtrait-associated SNPs in dbGaP and NHGRI downloaded from Association Results Browser
- traseR::taSNPLDlinkage disequilibrium (>0.8) within 100kb SNPs of all trait-associated SNPs from dbGaP and NHGRI
- traviz::countsA count matrix, used for testing.
- traviz::crvA SlingshotDataset object, used for testing.
- traviz::sceA SingleCellExperiment object, used for testing.
- TreeAndLeaf::phylo_speciesSpecies metadata from STRING-db v11
- TreeAndLeaf::phylo_treeSpecies tree from STRING-db v11
- TreeAndLeaf::spdataGenome statistics for eukaryotes with complete genome sequence
- treekoR::DeBiasi_COVID_CD8_sampCOVID-19 Sample data
- TreeSummarizedExperiment::tinyTreeA simulated phylogenetic tree with 10 tips and 9 internal nodes
- TREG::sce_zero_testTest SummarizedExperiment data
- Trendy::trendyExampleDataExample dataset for Trendy
- TRESS::BasalBin-level and region-level data from basal mouse brain samples
- TRESS::DMR_M3vsWTTranscriptome location and read counts of 200 candidate DMRs, and size factors.
- TRESS::DMR_SixWeekvsTwoWeekTranscriptome location and read counts of 200 candidate DMRs.
- tricycle::RevelioGeneList5 stage cell cycle gene marker list from Revelio
- tricycle::neuroRefPre-learned reference projection matrix from the Neurosphere dataset
- tricycle::neurosphere_exampleExample SingleCellExperiment dataset
- trigger::yeastA yeast data set for Transcriptional Regulation Inference from Genetics of Gene ExpRession
- trio::LDdataCase-Parent Trio Data
- trio::freq.hapCase-Parent Trio Data
- trio::mat.testCase-Parent Trio Data
- trio::prob.mat.testCase-Parent Trio Data
- trio::simuBkMapCase-Parent Trio Data
- trio::step3wayCase-Parent Trio Data
- trio::trio.gen.errCase-Parent Trio Data
- trio::trio.gen1Case-Parent Trio Data
- trio::trio.gen2Case-Parent Trio Data
- trio::trio.ped.errCase-Parent Trio Data
- trio::trio.ped1Case-Parent Trio Data
- trio::trio.ped2Case-Parent Trio Data
- tRNA::grtRNA example data
- tRNA::gr_ecotRNA example data
- tRNA::gr_humantRNA example data
- tRNA::gr_human2tRNA example data
- TRONCO::aCMLAtypical chronic myeloid leukemia dataset
- TRONCO::crc_gisticGISTIC example data
- TRONCO::crc_mafMAF example data
- TRONCO::crc_plainPlain mutation dataset
- TRONCO::mafMAF example data
- TRONCO::mutsSimple mutation dataset
- TRONCO::stageStage information for test_dataset
- TRONCO::test_datasetA complete dataset with hypotheses
- TRONCO::test_dataset_no_hyposA complete dataset
- TRONCO::test_modelA complete dataset with a reconstructed model
- TRONCO::test_model_kfoldA complete dataset with a reconstructed model and crossvalidation informations
- TSAR::example_tsar_dataExample tsar_data file
- TSAR::qPCR_data1qPCR_data1 Dataset
- TSAR::qPCR_data2qPCR_data2 Dataset
- TSAR::well_informationexample well information Data
- TSAR::well_information_templateWell Information Template
- TSCAN::lpsdataSinlge-cell RNA-seq data for BMDC cells before and after LPS stimulation
- TurboNorm::methylationCpG island DNA methylation array data
- tweeDEseq::seizureEpileptic seizure counts
- twilight::exfdrExample of twilight result
- twilight::expvalExample of twilight.pval result
- twoddpcr::KRAScountsKRAS mutant and wild type droplet counts and Poisson estimates.
- twoddpcr::KRAScountsQSKRAS mutant and wild type droplet counts and Poisson estimates.
- twoddpcr::KRAScountsWellColKRAS mutant and wild type droplet counts and Poisson estimates.
- twoddpcr::KRASdataDroplet amplitude data for KRAS mutant and wild type molecules.
- UCell::sample.matrixSample dataset to test UCell installation
- UMI4Cats::ex_ciita_umi4cContacs with CIITA promoter
- UNDO::BiologicalMixMCF7HS27MCF7 and HS27 biologically mixed
- UNDO::NumericalMixMCF7HS27MCF7 and HS27 numerically mixed
- UNDO::NumericalMixingMatrixmixing matrix of data NumericalMixMCF7HS27
- UNDO::PureMCF7HS27pure MCF7 and HS27
- unifiedWMWqPCR::NBdataDocumentation for the dataset NBdata
- unifiedWMWqPCR::NBgroupsDocumentation for the dataset NBdata
- unifiedWMWqPCR::NBmatDocumentation for the dataset NBdata
- universalmotif::ArabidopsisMotifArabidopsis motif in 'universalmotif' format.
- universalmotif::ArabidopsisPromotersArabidopsis promoters as a 'DNAStringSet'.
- universalmotif::JASPAR2018_CORE_DBSCORESJASPAR2018 CORE database scores
- universalmotif::examplemotifExample motif in 'universalmotif' format.
- universalmotif::examplemotif2Another example motif in 'universalmotif' format.
- universalmotif::fontDFrobotoPolygon coordinates for plotting letters.
- UPDhmm::hmmHMM data for predicting UPD events in trio genomic data
- VanillaICE::snp_expAn example SnpArrayExperiment
- VarCon::gene2transcriptSmall data frame specifying a transcript to certain genes for synonymous use.
- VarCon::hbgDonor sequences and their HBS
- VarCon::hexHexamers and Z scores
- VarCon::referenceDnaStringSetSmall DNAStringset as exemplary reference genome sequence
- VarCon::transCoordSmall table as exemplary transcript table with exon coordinates
- variancePartition::countMatrixA simulated dataset of gene counts
- variancePartition::geneCountsSimulation dataset for examples
- variancePartition::geneExprSimulation dataset for examples
- variancePartition::infoSimulation dataset for examples
- variancePartition::metadataA simulated dataset of gene counts
- VariantTools::coverage_H1993Vignette Data
- VariantTools::coverage_H2073Vignette Data
- VariantTools::genome_p53Vignette Data
- VariantTools::p53Vignette Data
- VariantTools::tallies_H1993Vignette Data
- VariantTools::tallies_H2073Vignette Data
- VaSP::rice.bgRice ballgown object
- vbmp::BRCA12BRCA tumour dataset
- VDJdive::contigsSplitDataFrameList containing AIRR-seq (TCR) data for six cells
- veloviz::pancreasPancreas scRNA-seq data
- veloviz::velMERFISH velocity subset
- VennDetail::T2DMT2DM
- VERSO::inferenceResults obtained running VERSO on the provided input dataset.
- VERSO::variantsMutation data obtained by variant calling from raw data of a selected set of SARS-CoV-2 samples available from NCBI BioProject PRJNA610428.
- vidger::df.cuffA 'cuffdiff' example dataset
- vidger::df.deseqA 'DESeq2' example dataset
- vidger::df.edgerA 'edgeR' example dataset
- ViSEAGO::myGOsmyGOs dataset
- vissE::hgscThe Hallmark collection from the MSigDB
- Voyager::ditto_colorsColorblind friendly palette from dittoSeq
- VplotR::ABF1_sacCer3ABF1_sacCer3
- VplotR::ATAC_ce11_Serizay2020ATAC_ce11_Serizay2020
- VplotR::CTCF_hg38CTCF_hg38
- VplotR::MNase_sacCer3_Henikoff2011MNase_sacCer3_Henikoff2011
- VplotR::MNase_sacCer3_Henikoff2011_subsetMNase_sacCer3_Henikoff2011_subset
- VplotR::REB1_sacCer3REB1_sacCer3
- VplotR::bam_testbam_test
- VplotR::ce11_all_REsce11_all_REs
- VplotR::ce11_promsce11_proms
- vsclust::artificial_clustersSynthetic/artificial data comprising 5 clusters
- vsclust::protein_expressionsData from a typical proteomics experiment
- vsn::kidneyIntensity data for one cDNA slide with two adjacent tissue samples from a nephrectomy (kidney)
- vsn::lymphomaIntensity data for 8 cDNA slides with CLL and DLBL samples from the Alizadeh et al. paper in Nature 2000
- vtpnet::cancerMapvariant-transcription factor-phenotype networks
- vtpnet::maurGWASvariant-transcription factor-phenotype networks
- vtpnet::pax4variant-transcription factor-phenotype networks
- vtpnet::pax4_75variant-transcription factor-phenotype networks
- vtpnet::pax4_85variant-transcription factor-phenotype networks
- wateRmelon::ageCoefs
- wateRmelon::coefAge Prediction from methylomic expression data
- wateRmelon::epic.controlsreadEPIC
- wateRmelon::epicV2.controls
- wateRmelon::hannumCoefAge Prediction from methylomic expression data
- wateRmelon::iDMRImprinting differentially methylated region probes of Illumina 450 arrays
- wateRmelon::melonSmall MethyLumi data set for examples and testing
- wateRmelon::sex_coef
- wateRmelon::smokp_cpgsSmoking Prediction from methylomic expression data
- wavClusteR::modelComponents of the non-parametric mixture moodel fitted on Ago2 PAR-CLIP data
- weitrix::simweiSimulated weitrix dataset.
- wiggleplotr::ncoa7_cdssCoding sequences from 9 protein coding transcripts of NCOA7
- wiggleplotr::ncoa7_exonsExons from 9 protein coding transcripts of NCOA7
- wiggleplotr::ncoa7_metadataGene metadata for NCOA7
- wpm::data_testFictitious clinical data for demonstration.
- xcms::faahko_subLC-MS preprocessing result test data sets
- xcms::faahko_sub2LC-MS preprocessing result test data sets
- xcms::xdataLC-MS preprocessing result test data sets
- xcms::xmseLC-MS preprocessing result test data sets
- xcore::remap_minixcore example molecular signatures
- xcore::rinderpest_minixcore example expression data
- XDE::expressionSetListExample of ExpressionSetList
- XDE::xmcmcObject of class XdeMcmc
- Xeva::PDXMIPDX-MI data
- Xeva::brcaPDXE breast cancer dataset
- Xeva::repdxExample PDX dataset
- XINA::example_clustersRandomly generated example datasets for XINA users. A dataset containing the XINA clustering results.
- XINA::gnA character vector containing 19,396 human genes This is for the randome data generation of XINA
- XINA::gn_descA character vector containing 19,396 human gene descriptions This is for the randome data generation of XINA
- XINA::hprd_ppiProtein-protein interaction resource downloaded from HPRD DB A data frame containing HRPD protein-protein interaction data
- XINA::string_exampleProtein-protein interaction resource downloaded from STRING DB for XINA's example dataset A data frame containing protein-protein interactions
- XINA::xina_result_examplePreviously processed xina analysis using XINA's random example data A list containing 'xina_analysis' results
- xmapbridge::exon.dataSample exon array dataset
- XNAString::complementary_basesDefault XNAString complementarity dictionary
- XNAString::xna_dictionaryDefault XNAString dictionary
- yamss::cmsRawExampleAn example cmsRaw object
- YAPSA::AlexCosmicArtif_sigInd_dfData for mutational signatures
- YAPSA::AlexCosmicArtif_sig_dfData for mutational signatures
- YAPSA::AlexCosmicValid_sigInd_dfData for mutational signatures
- YAPSA::AlexCosmicValid_sig_dfData for mutational signatures
- YAPSA::AlexCosmicValid_sig_dfData for mutational signatures
- YAPSA::AlexInitialArtif_sigInd_dfData for mutational signatures
- YAPSA::AlexInitialArtif_sig_dfData for mutational signatures
- YAPSA::AlexInitialValid_sigInd_dfData for mutational signatures
- YAPSA::AlexInitialValid_sig_dfData for mutational signatures
- YAPSA::COSMIC_subgroups_dfTest and example data
- YAPSA::GenomeOfNl_rawExample data for the Indel vignette
- YAPSA::MutCat_indel_dfExample mutational catalog for the Indel vignette
- YAPSA::PCAWG_SP_ID_sigInd_dfData for PCAWG SNV signatures (COSMIC v3), including artifacts 'PCAWG_SP_SBS_sigs_Artif_df': Data frame of the signatures published by Alexandrov et al. (Biorxiv 2013) which were decomposed with the method SigProfiler. SNV signatures are labeled with SBS, single base signature. There are 67 signatures which constitute the columns, 47 of which were validated by a bayesian NFM mehtod, SignatureAnayzer. Validated signatures are SBS1-SBS26,SBS28-SBS42 and SBS44. SBS7 is split up into 7 a/b/c and d. SBS10 ans SBS17 are both split up into a and b. Resulting in a 47 validated sigantures. Please note, unlike the paper by Alexandrov et al. (Biorxiv 2018) the data sets do not contain a SBS84 and SBS85 as not all were availiablt to perfom supervised signature analysis. In total there are 96 different features and therefore 96 rows when dealing with a trinucleotide context.
- YAPSA::PCAWG_SP_ID_sigs_dfData for PCAWG SNV signatures (COSMIC v3), including artifacts 'PCAWG_SP_SBS_sigs_Artif_df': Data frame of the signatures published by Alexandrov et al. (Biorxiv 2013) which were decomposed with the method SigProfiler. SNV signatures are labeled with SBS, single base signature. There are 67 signatures which constitute the columns, 47 of which were validated by a bayesian NFM mehtod, SignatureAnayzer. Validated signatures are SBS1-SBS26,SBS28-SBS42 and SBS44. SBS7 is split up into 7 a/b/c and d. SBS10 ans SBS17 are both split up into a and b. Resulting in a 47 validated sigantures. Please note, unlike the paper by Alexandrov et al. (Biorxiv 2018) the data sets do not contain a SBS84 and SBS85 as not all were availiablt to perfom supervised signature analysis. In total there are 96 different features and therefore 96 rows when dealing with a trinucleotide context.
- YAPSA::PCAWG_SP_SBS_sigInd_Artif_dfData for PCAWG SNV signatures (COSMIC v3), including artifacts 'PCAWG_SP_SBS_sigs_Artif_df': Data frame of the signatures published by Alexandrov et al. (Biorxiv 2013) which were decomposed with the method SigProfiler. SNV signatures are labeled with SBS, single base signature. There are 67 signatures which constitute the columns, 47 of which were validated by a bayesian NFM mehtod, SignatureAnayzer. Validated signatures are SBS1-SBS26,SBS28-SBS42 and SBS44. SBS7 is split up into 7 a/b/c and d. SBS10 ans SBS17 are both split up into a and b. Resulting in a 47 validated sigantures. Please note, unlike the paper by Alexandrov et al. (Biorxiv 2018) the data sets do not contain a SBS84 and SBS85 as not all were availiablt to perfom supervised signature analysis. In total there are 96 different features and therefore 96 rows when dealing with a trinucleotide context.
- YAPSA::PCAWG_SP_SBS_sigInd_Real_dfData for PCAWG SNV signatures (COSMIC v3), including artifacts 'PCAWG_SP_SBS_sigs_Artif_df': Data frame of the signatures published by Alexandrov et al. (Biorxiv 2013) which were decomposed with the method SigProfiler. SNV signatures are labeled with SBS, single base signature. There are 67 signatures which constitute the columns, 47 of which were validated by a bayesian NFM mehtod, SignatureAnayzer. Validated signatures are SBS1-SBS26,SBS28-SBS42 and SBS44. SBS7 is split up into 7 a/b/c and d. SBS10 ans SBS17 are both split up into a and b. Resulting in a 47 validated sigantures. Please note, unlike the paper by Alexandrov et al. (Biorxiv 2018) the data sets do not contain a SBS84 and SBS85 as not all were availiablt to perfom supervised signature analysis. In total there are 96 different features and therefore 96 rows when dealing with a trinucleotide context.
- YAPSA::PCAWG_SP_SBS_sigs_Artif_dfData for PCAWG SNV signatures (COSMIC v3), including artifacts 'PCAWG_SP_SBS_sigs_Artif_df': Data frame of the signatures published by Alexandrov et al. (Biorxiv 2013) which were decomposed with the method SigProfiler. SNV signatures are labeled with SBS, single base signature. There are 67 signatures which constitute the columns, 47 of which were validated by a bayesian NFM mehtod, SignatureAnayzer. Validated signatures are SBS1-SBS26,SBS28-SBS42 and SBS44. SBS7 is split up into 7 a/b/c and d. SBS10 ans SBS17 are both split up into a and b. Resulting in a 47 validated sigantures. Please note, unlike the paper by Alexandrov et al. (Biorxiv 2018) the data sets do not contain a SBS84 and SBS85 as not all were availiablt to perfom supervised signature analysis. In total there are 96 different features and therefore 96 rows when dealing with a trinucleotide context.
- YAPSA::PCAWG_SP_SBS_sigs_Real_dfData for PCAWG SNV signatures (COSMIC v3), including artifacts 'PCAWG_SP_SBS_sigs_Artif_df': Data frame of the signatures published by Alexandrov et al. (Biorxiv 2013) which were decomposed with the method SigProfiler. SNV signatures are labeled with SBS, single base signature. There are 67 signatures which constitute the columns, 47 of which were validated by a bayesian NFM mehtod, SignatureAnayzer. Validated signatures are SBS1-SBS26,SBS28-SBS42 and SBS44. SBS7 is split up into 7 a/b/c and d. SBS10 ans SBS17 are both split up into a and b. Resulting in a 47 validated sigantures. Please note, unlike the paper by Alexandrov et al. (Biorxiv 2018) the data sets do not contain a SBS84 and SBS85 as not all were availiablt to perfom supervised signature analysis. In total there are 96 different features and therefore 96 rows when dealing with a trinucleotide context.
- YAPSA::chosen_signatures_indices_dfTest and example data
- YAPSA::cutoffCosmicArtif_abs_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffCosmicArtif_rel_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffCosmicValid_abs_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffCosmicValid_rel_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffInitialArtif_abs_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffInitialArtif_rel_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffInitialValid_abs_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffInitialValid_rel_dfCutoffs for a supervised analysis of mutational signatures.
- YAPSA::cutoffPCAWG_ID_WGS_Pid_dfOpt. cutoffs, PCAWG SNV signatures, including artifacts
- YAPSA::cutoffPCAWG_SBS_WGSWES_artifPid_dfOpt. cutoffs, PCAWG SNV signatures, including artifacts
- YAPSA::cutoffPCAWG_SBS_WGSWES_realPid_dfOpt. cutoffs, PCAWG SNV signatures, including artifacts
- YAPSA::exchange_colour_vectorColours codes for displaying SNVs
- YAPSA::exome_mutCatRaw_dfExample mutational catalog for the exome vignette
- YAPSA::lymphomaNature2013_mutCat_dfExample mutational catalog for the SNV vignette
- YAPSA::lymphoma_Nature2013_COSMIC_cutoff_exposures_dfTest and example data
- YAPSA::lymphoma_Nature2013_raw_dfTest and example data
- YAPSA::lymphoma_PID_dfTest and example data
- YAPSA::lymphoma_test_dfTest and example data
- YAPSA::rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_dfTest and example data
- YAPSA::targetCapture_cor_factorsCorrection factors for different target capture kits
- yarn::bladderBladder RNA-seq data from the GTEx consortium
- yarn::skinSkin RNA-seq data from the GTEx consortium
- zinbwave::toydataToy dataset to check the model
- zitools::mtxMatrix Data
- ZygosityPredictor::GR_GENE_MODELgermline small variant object
- ZygosityPredictor::GR_GERM_SMALL_VARSgermline small variant object
- ZygosityPredictor::GR_HAPLOBLOCKShaploblocks
- ZygosityPredictor::GR_SCNAcopynumber object
- ZygosityPredictor::GR_SOM_SMALL_VARSsomatic small variant object
