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stream)a4a4Basea4Classifa4Corea4Preproca4ReportingABarrayabseqRABSSeqacdeACEaCGHACMEADaCGH2ADAMADAMguiADAPTadductomicsRADImputeadSplitadverSCarialAerithAffiXcanaffxparseraffyaffycompaffyContamaffycoretoolsaffyILMaffyioaffylmGUIaffyPLMAffyRNADegradationAGDEXaggregateBioVaragilpAgiMicroRnaAHMassBankAIMSairpartalabasteralabaster.basealabaster.bumpyalabaster.filesalabaster.maealabaster.matrixalabaster.rangesalabaster.scealabaster.schemasalabaster.sealabaster.sfealabaster.spatialalabaster.stringalabaster.vcfALDEx2alevinQCAllelicImbalanceAlphaBetaAlphaMissenseRAlpsNMRaltcdfenvsAMARETTOAMOUNTAINamplicananansiAnaquinANCOMBCANFanglemaniaanimalculesannaffyanndataRannmapannoLinkerannotateAnnotationDbiAnnotationFilterAnnotationForgeAnnotationHubAnnotationHubDataannotationToolsannotatranotaanota2seqantiProfilesAnVILAnVILAzAnVILBaseAnVILBillingAnVILGCPAnVILPublishAnVILVRSAnVILWorkflowapComplexapeglmAPLappreci8Raroma.lightArrayExpressarrayMvoutarrayQualityarrayQualityMetricsARRmNormalizationartMSASAFEASEBASGSCAASICSASpliAssessORFASSETASSIGNassortheadASURATasuriatacInferCnvATACseqQCATACseqTFEAatenaatSNPattractAUCellaugere.coreaugere.deaugere.gseaaugere.screenaugere.soloautonomicsAWAggregatorAWFisherawstBaalChIPbaconBADERBadRegionFinderBAGSbambuBamScalebamsignalsBANDITSbandleBanksybanoccbarbieQBaseSpaceRBasic4CseqBASiCSBASiCStanBasicSTARRseqbasiliskbasilisk.utilsbatchCorrBatChefbatchelorBatchQCBatchSVGBattlefieldBayesKnockdownBayesSpacebayNormbaySeqBBCAnalyzerBCRANKbcSeqbeachmatbeachmat.hdf5beachmat.tiledbbeadarrayBeadDataPackRBEATBEclearbedbaserbeerbenchdamicBERTbetaHMMbetterChromVARbettrBG2BgeeCallBgeeDBBicAREBiFETbigmelonBindingSiteFinderbioassayRBiobasebiobtreeRBioc.gffbioCancerBioCartaImageBiocAzulBiocBaseUtilsBiocBookBiocBuildReporterBiocCheckBiocFHIRBiocFileCacheBiocGenericsbiocGraphBiocHailBiocHubsShinyBiocIOBiocMaintainerAppbiocmakeBiocNeighborsBioCorBiocParallelBiocPkgDashBiocPkgToolsbiocroxytestBiocSetBiocSingularBiocSklearnBiocStylebiocthisBiocVersionbiocViewsBiocWorkflowToolsbiodbbioDistBioGAbiomaRtbiomformatBioMVCClassbiomvRCNSBioNARBioNEROBioNetBioQCbiosignerBiostringsBioTIPbiotmlebiovizBasebiscuiteerBiSeqblacksheeprblaseblimaBLMABloodGen3ModuleblusterbnbcbnemBOBaFITborealisBRAINbranchpointerbreakpointRBreastSubtypeRbrendaDbBREW3R.rBridgeDbRbroadSeqBrowserVizBSgenomeBSgenomeForgebsseqBufferedMatrixBufferedMatrixMethodsbugsigdbrBulkSignalRBUMHMMbumphunterBumpyMatrixBUSBUScorrectBUSpaRseBUSseqCaDrACAENCAFECAGEfightRcageminerCAGErCalibraCurvecalmCAMERACaMutQCcanceRcancerclasscardelinoCardinalCardinalIOCARDspacarnationCARNIVALcasperCATALYSTCategorycategoryCompareCatsCradleCausalRcbafcBioPortalDataCBN2PathCBNplotcbpManagerCCAFEccfindRccImputeCCPlotRCCPROMISECDIcelarefceldaCellBarcodecellbaseRCellBenchcellityCellMapperCellMentorcellmigcellmigRationCellMixSCellNOptRcellscapeCellTrailscellxgenedpCEMiToolcenscytCepoceRNAnetsimCeTFCexoRCFAssaycfdnakitcfDNAProcfToolsCGENCGHbaseCGHcallcghMCRCGHnormaliterCGHregionsChAMPChemmineOBChemmineRCHETAHchevreulPlotchevreulProcesschevreulShinyChicagochihayachimeravizChIPanalyserChIPCompchipenrichChIPexoQualChIPpeakAnnoChIPQCChIPseekerchipseqChIPseqRChIPsimChIPXpresschopsticksChromatogramschromDrawChromHeatMapchromPlotChromSCapechromVARCHRONOScicerocigarilloCIMICEcircRNAprofilerCircSeqAlignTkCiteFuseClassifyRcleanUpdTSeqCleanUpRNAseqcleaverclevRvisclippdaclippercliProfilercliqueMSClomialClonalSimclstclstutilsCluMSIDClustAllclustCompclusterExperimentClusterFoldSimilarityClusterGVisClusterJudgeclusterProfilerclusterSeqClusterSignificanceclusterStabclustifyrClustIRRclustSIGNALCMAcmapRcn.farmscn.mopsCNAnormCNErCNORdtCNORfeederCNORfuzzyCNORodeCNToolsCNVfilteRcnvGSACNVizCNVMetricsCNVPanelizerCNVRangerCNVrd2CoCiteStatsCOCOAcodelinkCODEXCoGAPScogenacogeqcCogitocoGPScolacomaprcombicoMethDMRCOMPASScompcodeRCompensAIDcompEpiToolsComplexHeatmapCompoundDbComPrAncompSPOTconcordexRcondimentsCONFESSconsensusConsensusClusterPlusconsensusDEconsensusOVconsensusSeekeRconsICACONSTANdconumeeconvertcopaCopyNumberPlotsCoralysiscoRdonCoreGxCormotifcorralcoseqCoSIAcosmiqcosmosRCOSNetCOTANcountsimQCcovEBCoverageViewcovRNACPSMcpvSNPcqnCrcBiomeScreenCRImageCRISPRballcrisprBasecrisprBowtiecrisprBwacrisprDesigncrisprScoreCRISPRseekcrisprShinyCrispRVariantscrisprVersecrisprVizcrlmmcrumblrcrupRCSARcsawcsdRCSOACSSQctcCTdataCTDquerierCTexploreRcTRAPctsGECTSVcustomCMPdbcustomProDBcyanoFiltercyclecydarcypressCytoDxCyTOFpowercytofQCCytoGLMMcytoKernelcytolibcytomapperCytoMDScytoMEMCytoMLCytoPipelineCytoPipelineGUIcytoviewerdada2dagLogodaMADAMEfinderdamidBindDaMiRseqDamseldandelionRDAPARDaparToolsheddarDARTdcanrDCATSdcGSAddCtddPCRclustdearseqdebrowserdecemedipDECIPHERdecompTumor2SigdecontamdecontXDeconvoBuddiesdeconvRdecoupleRDeeDeeExperimentDeepPINCSdeepSNVDeepTargetDEFormatsDegCreDegNormDEGraphDEGreportDEGseqDelayedArrayDelayedDataFrameDelayedMatrixStatsDelayedRandomArrayDelayedTensorDELocaldeltaCaptureCdeltaGsegDeMANDDeMixTdemuxmixdemuxSNPDenoISTdensvisDepecheRDepInfeRDEqMSderfinderderfinderHelperderfinderPlotDEScan2DE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a4Base::nlcvTT (nlcv)ABSSeq::simuN5 (list)acde::phytophthora (list)ACE::copyNumbersSegmented (QDNAseqCopyNumbers)aCGH::colorectal (aCGH)aCGH::ex.acgh.hmm (list)ACME::example.agff (ACMESet)ADaCGH2::inputEx (data.frame)ADaCGH2::inputEx-sp (data.frame)ADAM::ExpressionAedes (data.frame)ADAM::KeggPathwaysAedes (data.frame)ADAMgui::DiffAedes (data.frame)ADAMgui::GeneFunctionAedes (data.frame)ADAMgui::ResultAnalysisAedes (data.frame)ADAPT::ecc_plaque (phyloseq)ADAPT::ecc_saliva (phyloseq)ADImpute::demo_data (dgCMatrix)ADImpute::demo_net (matrix)ADImpute::demo_sce (SingleCellExperiment)ADImpute::network.coefficients (dgCMatrix)ADImpute::transcript_length (data.frame)adSplit::golubKEGGSplits (splitSet)AffiXcan::exprMatrix (SummarizedExperiment)AffiXcan::regionAssoc (data.frame)AffiXcan::trainingCovariates (data.frame)affy::cdfenv.example (environment)affy::mapCdfName (data.frame)affy::SpikeIn (ProbeSet)affycomp::dilution.phenodata (AnnotatedDataFrame)affycomp::hgu133a.spikein.phenodata (AnnotatedDataFrame)affycomp::hgu133a.spikein.xhyb (list)affycomp::mas5.assessment (list)affycomp::spikein.phenodata (AnnotatedDataFrame)AGDEX::agdex.res (list)AGDEX::gset.data (GeneSetCollection)AGDEX::human.data (ExpressionSet)AGDEX::map.data (list)AGDEX::mouse.data (ExpressionSet)aggregateBioVar::small_airway (SingleCellExperiment)AgiMicroRna::dd.micro (uRNAList)AgiMicroRna::ddPROC (uRNAList)AgiMicroRna::targets.micro (data.frame)AIMS::AIMSmodel (list)AIMS::mcgillExample (list)ALDEx2::selex (data.frame)ALDEx2::synth2 (data.frame)AllelicImbalance::ASEset (ASEset)AllelicImbalance::ASEset.sim (ASEset)AllelicImbalance::genomatrix (matrix)AllelicImbalance::GRvariants (GRanges)AllelicImbalance::reads (GAlignmentsList)AlpsNMR::hmdb (tbl_df)AlpsNMR::HMDB_blood (data.frame)AlpsNMR::HMDB_cell (data.frame)AlpsNMR::HMDB_urine (data.frame)AlpsNMR::Parameters_blood (data.frame)AlpsNMR::Parameters_cell (data.frame)AlpsNMR::Parameters_urine (data.frame)AlpsNMR::ROI_blood (data.frame)AlpsNMR::ROI_cell (data.frame)AlpsNMR::ROI_urine (data.frame)altcdfenvs::cdfenvEx (CdfEnvAffy)AMARETTO::BatchData (data.frame)AMARETTO::Driver_Genes (list)AMARETTO::MsigdbMapping (data.frame)AMARETTO::ProcessedDataLIHC (list)anansi::ec2cpd (data.frame)anansi::ec2ko (data.frame)anansi::FMT_KOs (data.frame)anansi::FMT_metab (data.frame)anansi::FMT_metadata (data.frame)anansi::krebs (data.frame)Anaquin::RnaQuinGeneMixture (data.frame)Anaquin::RnaQuinIsoformMixture (data.frame)Anaquin::UserGuideData_5.4.5.1 (data.frame)Anaquin::UserGuideData_5.4.6.3 (data.frame)Anaquin::UserGuideData_5.6.3 (data.frame)ANCOMBC::QMP (matrix)annaffy::aafExpr (ExpressionSet)annotate::hgByChroms (list)annotate::hgCLengths (numeric)annotate::hgu95Achroloc (environment)annotate::hgu95Achrom (environment)annotate::hgu95All (environment)annotate::hgu95AProbLocs (chromLocation)annotate::hgu95Asym (environment)annotationTools::annot_HGU133A (data.frame)annotationTools::ortho (data.frame)annotationTools::table_human (data.frame)annotationTools::table_mouse (data.frame)annotatr::annotations (GRanges)anota::anotaDataP (matrix)anota::anotaDataT (matrix)anota::anotaPhenoVec (character)anota2seq::anota2seq_data_P (matrix)anota2seq::anota2seq_data_T (matrix)anota2seq::anota2seq_pheno_vec (character)AnVILBilling::demo_rec (avReckoning)apComplex::apEX (matrix)apComplex::apEXG (graphNEL)apComplex::gavin06FilteredEstimates (list)apComplex::gavinBP2006 (matrix)apComplex::HMSPCI (matrix)apComplex::HMSPCIgraph (graphNEL)apComplex::Krogan (matrix)apComplex::krogan06FilteredEstimates (list)apComplex::kroganBPMat2006 (matrix)apComplex::MBMEcHMSPCI (matrix)apComplex::MBMEcKrogan (matrix)apComplex::MBMEcTAP (matrix)apComplex::SBMHcHMSPCI (matrix)apComplex::SBMHcTAP (matrix)apComplex::TAP (matrix)apComplex::TAPgraph (graphNEL)apComplex::UnRBBcHMSPCI (matrix)apComplex::UnRBBcTAP (matrix)apComplex::yNameTAP (matrix)apComplex::yTAP (list)arrayMvout::afxsubDEG (list)arrayMvout::fig3map (numeric)arrayMvout::ilmQA (matrix)arrayMvout::itnQA (data.frame)arrayMvout::maqcQA (data.frame)arrayMvout::s12cDEG (list)arrayMvout::spikQA (data.frame)arrayQuality::HsReferenceDB (matrix)arrayQuality::MmDEGenes (data.frame)arrayQuality::MmReferenceDB (matrix)ARRmNormalization::ProbesType (data.frame)artMS::artms_config (list)artMS::artms_data_corum_mito_database (data.frame)artMS::artms_data_pathogen_LPN (data.frame)artMS::artms_data_pathogen_TB (data.frame)artMS::artms_data_ph_config (list)artMS::artms_data_ph_contrast (character)artMS::artms_data_ph_evidence (data.frame)artMS::artms_data_ph_keys (data.frame)artMS::artms_data_ph_msstats_modelqc (data.frame)artMS::artms_data_ph_msstats_results (data.frame)artMS::artms_data_randomDF (data.frame)ASAFE::adm_ancestries_test (data.frame)ASAFE::adm_genotypes_test (data.frame)ASGSCA::B0 (matrix)ASGSCA::GenPhen (data.frame)ASGSCA::QCAHS (data.frame)ASGSCA::ResQCAHS (list)ASGSCA::W0 (matrix)ASICS::pure_library (PureLibrary)ASSET::betahat (numeric)ASSET::data (data.frame)ASSET::data (data.frame)ASSET::ldscintmat (matrix)ASSET::N00 (matrix)ASSET::N10 (matrix)ASSET::N11 (matrix)ASSET::Neff (numeric)ASSET::SE (numeric)ASSET::SNP (character)ASSET::traits (character)ASSIGN::excludegenes (character)ASSIGN::geneList1 (list)ASSIGN::gfrn_geneList (list)ASSIGN::testData1 (data.frame)ASSIGN::trainingData1 (data.frame)ASURAT::human_COMSig_eg (list)ASURAT::human_GO_eg (list)ASURAT::human_KEGG_eg (list)ASURAT::pbmc_eg (SingleCellExperiment)ASURAT::pbmcs_eg (list)asuri::ex_genePheno (list)asuri::ex_patientRisk (list)asuri::ex_predictPatientRisk (data.frame)asuri::ex_prefilterSAM (character)asuri::seBRCA (SummarizedExperiment)atSNP::encode_motif (list)atSNP::encode_motifinfo (character)atSNP::jaspar_motif (list)atSNP::jaspar_motifinfo (character)atSNP::motif_library (list)atSNP::motif_match (data.frame)atSNP::motif_scores (list)atSNP::prior (numeric)atSNP::snp_tbl (data.frame)atSNP::snpInfo (list)atSNP::transition (matrix)attract::exprs.dat (matrix)attract::loring.eset (ExpressionSet)attract::samp.info (data.frame)attract::subset.loring.eset (ExpressionSet)AWAggregator::sample.prot.PD (data.frame)AWAggregator::sample.PSM.FP (data.frame)AWAggregator::sample.PSM.PD (data.frame)AWFisher::data_mouseMetabolism (list)BaalChIP::BaalObject (BaalChIP)BaalChIP::blacklist_hg19 (GRanges)BaalChIP::ENCODEexample (BaalChIP)BaalChIP::FAIREexample (BaalChIP)BaalChIP::pickrell2011cov1_hg19 (GRanges)BaalChIP::UniqueMappability50bp_hg19 (GRanges)BAGS::AnnotationMFGO (list)BANDITS::gene_tr_id (data.frame)BANDITS::input_data (BANDITS_data)BANDITS::precision (list)BANDITS::results (BANDITS_test)Banksy::hippocampus (list)Banksy::rings (SpatialExperiment)banocc::compositions_hard_null (matrix)banocc::compositions_neg_spike (matrix)banocc::compositions_null (matrix)banocc::compositions_pos_spike (matrix)banocc::counts_hard_null (matrix)banocc::counts_neg_spike (matrix)banocc::counts_null (matrix)banocc::counts_pos_spike (matrix)barbieQ::monkeyHSPC (SummarizedExperiment)BaseSpaceR::aAuth (AppAuth)Basic4Cseq::liverData (Data4Cseq)Basic4Cseq::liverDataRaw (Data4Cseq)BASiCS::ChainRNA (BASiCS_Chain)BASiCS::ChainRNAReg (BASiCS_Chain)BASiCS::ChainSC (BASiCS_Chain)BASiCS::ChainSCReg (BASiCS_Chain)batchCorr::meta (data.frame)batchCorr::PTfill (matrix)batchCorr::PTnofill (matrix)BatchQC::batch_indicator (data.frame)BatchQC::merged_IDs (data.frame)BatchQC::protein_data (data.frame)BatchQC::protein_sample_info (data.frame)BatchQC::signature_data (data.frame)BatchSVG::list_batch_df (list)Battlefield::visium_simulated_spe (SpatialExperiment)Battlefield::visiumHD_16um_simulated_spe (SpatialExperiment)Battlefield::visiumHD_8um_simulated_spe (SpatialExperiment)BayesKnockdown::lincs.kd (matrix)bayNorm::EXAMPLE_DATA_list (list)baySeq::CDPost (countData)baySeq::CDPriors (countData)baySeq::mobAnnotation (data.frame)baySeq::mobData (matrix)baySeq::pairData (matrix)baySeq::simData (matrix)baySeq::zimData (matrix)BCRANK::BCRANKout (BCRANKresult)beadarray::metaTemplate (list)beadarray::platformSigs (list)BEAT::positions (data.frame)BEAT::positions.reference (data.frame)BEclear::ex.corrected.data (data.frame)BEclear::ex.data (matrix)BEclear::ex.samples (data.frame)benchdamic::microbial_metabolism (data.frame)benchdamic::ps_plaque_16S (phyloseq)benchdamic::ps_stool_16S (phyloseq)betaHMM::annotation_data (data.frame)betaHMM::pca_methylation_data (data.frame)betaHMM::sample_annotation_file (data.frame)betaHMM::sample_methylation_file (data.frame)BG2::kinship (matrix)BG2::SNPs (matrix)BG2::Y_binary (integer)BG2::Y_poisson (integer)BgeeDB::geneList (factor)BicARE::sample.bicData (ExpressionSet)BicARE::sample.biclustering (biclustering)bigmelon::cantaloupe (MethyLumiSet)bigmelon::honeydew (MethyLumiSet)bioassayR::samplebioassay (data.frame)Biobase::aaMap (data.frame)Biobase::geneCov (data.frame)Biobase::geneCovariate (data.frame)Biobase::geneData (matrix)Biobase::reporter (data.frame)Biobase::sample.ExpressionSet (ExpressionSet)Biobase::sample.MultiSet (MultiSet)Biobase::seD (matrix)Biobase::SW (RGList)bioCancer::epiGenomics (data.frame)bioCancer::user_CNA (data.frame)bioCancer::user_MetHM27 (data.frame)bioCancer::user_MetHM450 (data.frame)bioCancer::user_mRNA (data.frame)bioCancer::user_Mut (data.frame)BioCartaImage::BC2ENTREZ (data.frame)BioCartaImage::BIOCARTA_PATHWAYS (list)BioCartaImage::PATHWAY2BC (data.frame)BioCartaImage::PATHWAY2ENTREZ (data.frame)BioCartaImage::PATHWAY2MSIGDB (data.frame)BiocFHIR::allin (list)BiocHail::kg_3202 (data.frame)BiocHail::pcs_191k (data.frame)BiocHail::pcs_38k (data.frame)biocViews::biocViewsVocab (graphNEL)biomvRCNS::coriell (data.frame)biomvRCNS::encodeTP53 (list)biomvRCNS::variosm (GRanges)BioNAR::diseasome (igraph)BioNERO::filt.se (SummarizedExperiment)BioNERO::og.zma.osa (data.frame)BioNERO::osa.se (SummarizedExperiment)BioNERO::zma.interpro (data.frame)BioNERO::zma.se (SummarizedExperiment)BioNERO::zma.tfs (data.frame)BioNet::pvaluesExample (matrix)biosigner::diaplasma (list)biosigner::SpikePos (list)Biostrings::BLOSUM100 (moved_to_pwalign_pkg)Biostrings::BLOSUM45 (moved_to_pwalign_pkg)Biostrings::BLOSUM50 (moved_to_pwalign_pkg)Biostrings::BLOSUM62 (moved_to_pwalign_pkg)Biostrings::BLOSUM80 (moved_to_pwalign_pkg)Biostrings::HNF4alpha (DNAStringSet)Biostrings::PAM120 (moved_to_pwalign_pkg)Biostrings::PAM250 (moved_to_pwalign_pkg)Biostrings::PAM30 (moved_to_pwalign_pkg)Biostrings::PAM40 (moved_to_pwalign_pkg)Biostrings::PAM70 (moved_to_pwalign_pkg)Biostrings::yeastSEQCHR1 (character)BioTIP::cod (data.frame)BioTIP::gencode (GRanges)BioTIP::GSE6136_cli (data.frame)BioTIP::GSE6136_matrix (data.frame)BioTIP::ILEF (data.frame)BioTIP::intron (GRanges)BioTIP::membersL (list)BioTIP::subcounts (list)biovizBase::crc.gr (GRanges)biovizBase::crc1.GeRL (SimpleGRangesList)biovizBase::darned_hg19_subset500 (GRanges)biovizBase::genesymbol (GRanges)biovizBase::hg19Ideogram (GRanges)biovizBase::hg19IdeogramCyto (GRanges)biovizBase::hg19sub (GRanges)biovizBase::ideo (list)biovizBase::ideoCyto (list)biovizBase::mut.gr (GRanges)biscuiteer::clocks (data.frame)biscuiteer::ENSR_subset.hg19 (GRanges)biscuiteer::ENSR_subset.hg38 (GRanges)biscuiteer::GRCh37.chromArm (GRanges)biscuiteer::GRCh38.chromArm (GRanges)biscuiteer::H9state23unmeth.hg19 (GRanges)biscuiteer::H9state23unmeth.hg38 (GRanges)biscuiteer::hg19.chromArm (GRanges)biscuiteer::hg38.chromArm (GRanges)biscuiteer::HMM_CpG_islands.hg19 (GRanges)biscuiteer::HMM_CpG_islands.hg38 (GRanges)biscuiteer::seqinfo.hg19 (Seqinfo)biscuiteer::seqinfo.hg38 (Seqinfo)biscuiteer::seqinfo.mm10 (Seqinfo)BiSeq::betaResults (data.frame)BiSeq::betaResultsNull (data.frame)BiSeq::DMRs (GRanges)BiSeq::predictedMeth (BSrel)BiSeq::promoters (GRanges)BiSeq::rrbs (BSraw)BiSeq::vario (list)blacksheepr::sample_annotationdata (data.frame)blacksheepr::sample_phosphodata (data.frame)blacksheepr::sample_rnadata (data.frame)blase::MCA_PF_SCE (SingleCellExperiment)blase::painter_microarray (data.frame)blase::tradeSeq_BLASE_example_sce (SingleCellExperiment)blase::zhang_2021_heat_shock_bulk (data.frame)BLMA::data_GSE17054 (data.frame)BLMA::data_GSE33223 (data.frame)BLMA::data_GSE42140 (data.frame)BLMA::data_GSE57194 (data.frame)BLMA::group_GSE17054 (character)BLMA::group_GSE33223 (character)BLMA::group_GSE42140 (character)BLMA::group_GSE57194 (character)bnbc::cgEx (ContactGroup)bnem::bcr (list)BOBaFIT::TCGA_BRCA_CN_segments (data.frame)BreastSubtypeR::AIMSmodel (list)BreastSubtypeR::BreastSubtypeRobj (list)BreastSubtypeR::Gene.ID.ann (data.frame)BreastSubtypeR::OSLO2EMIT0obj (list)BreastSubtypeR::sspbc.models (list)BreastSubtypeR::sspbc.models.fullname (list)BreastSubtypeR::TCGABRCAobj (list)brendaDb::acronyms (data.table)bsseq::BS.chr22 (BSseq)BulkSignalR::annotation.spa (DFrame)BulkSignalR::bodyMap.mouse (data.frame)BulkSignalR::bsrdm (BSRDataModel)BulkSignalR::bsrdm.comp (BSRDataModelComp)BulkSignalR::bsrdm.spa (BSRDataModel)BulkSignalR::bsrinf (BSRInference)BulkSignalR::bsrinf.comp (BSRInferenceComp)BulkSignalR::bsrinf.mouse (BSRInference)BulkSignalR::bsrinf.spa (BSRInference)BulkSignalR::immune.signatures (data.frame)BulkSignalR::ortholog.dict (data.frame)BulkSignalR::p.EMT (data.frame)BulkSignalR::sdc (data.frame)BulkSignalR::tme.signatures (data.frame)BUMHMM::covFile (data.frame)BUMHMM::docFile (data.frame)BUMHMM::dorFile (matrix)BUMHMM::se (SummarizedExperiment)BUMHMM::seq (character)bumphunter::TT (list)BUS::copasi (data.frame)BUS::tumors.miRNA (matrix)BUS::tumors.mRNA (matrix)BUScorrect::BUSexample_data (list)BUSpaRse::cellranger_biotypes (character)BUSpaRse::ensembl_gene_biotypes (character)BUSpaRse::ensembl_gff_mcols (character)BUSpaRse::ensembl_gtf_mcols (character)BUSpaRse::ensembl_tx_biotypes (character)BUSpaRse::refseq_gff_mcols (character)BUSseq::BUSseqfits_example (SingleCellExperiment)CaDrA::BRCA_GISTIC_MUT_SIG (SummarizedExperiment)CaDrA::CCLE_MUT_SCNA (SummarizedExperiment)CaDrA::CTNBB1_reporter (numeric)CaDrA::perm_res (list)CaDrA::sim_FS (SummarizedExperiment)CaDrA::sim_Scores (numeric)CaDrA::TAZYAP_BRCA_ACTIVITY (numeric)CaDrA::topn_list (list)CAEN::realData (SummarizedExperiment)CAFE::CAFE_data (list)CAGEfightR::exampleBidirectional (RangedSummarizedExperiment)CAGEfightR::exampleCTSSs (RangedSummarizedExperiment)CAGEfightR::exampleDesign (DFrame)CAGEfightR::exampleGenes (RangedSummarizedExperiment)CAGEfightR::exampleUnidirectional (RangedSummarizedExperiment)cageminer::chr_length (GRanges)cageminer::gcn (list)cageminer::gene_ranges (GRanges)cageminer::guides (data.frame)cageminer::hubs (data.frame)cageminer::mine2 (list)cageminer::mined_candidates (data.frame)cageminer::pepper_se (SummarizedExperiment)cageminer::snp_pos (GRanges)cageminer::tfs (data.frame)CAGEr::exampleCAGEexp (CAGEexp)CAGEr::exampleZv9_annot (GRanges)CAGEr::FANTOM5humanSamples (data.frame)CAGEr::FANTOM5mouseSamples (data.frame)calm::pso (data.frame)CAMERA::mm14 (xcmsSet)cancerclass::GOLUB (ExpressionSet)cancerclass::GOLUB1 (ExpressionSet)cardelino::A_clone (matrix)cardelino::A_germline (matrix)cardelino::Config_all (list)cardelino::D_clone (matrix)cardelino::D_germline (matrix)cardelino::D_input (matrix)cardelino::tree (phylo)cardelino::tree_3clone (phylo)cardelino::tree_4clone (phylo)cardelino::tree_5clone (phylo)CARDspa::markerList (list)CARDspa::sc_count (dgCMatrix)CARDspa::sc_meta (data.frame)CARDspa::spatial_count (dgCMatrix)CARDspa::spatial_location (data.frame)carnation::degpatterns_dex (list)carnation::eres_cell (enrichResult)carnation::eres_dex (enrichResult)carnation::res_cell (DESeqResults)carnation::res_dex (DESeqResults)casper::distrsGSE37704 (list)casper::hg19DB (annotatedGenome)casper::K562.r1l1 (list)CATALYST::isotope_list (list)CATALYST::merging_table (tbl_df)CATALYST::mp_cells (flowFrame)CATALYST::PBMC_fs 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(rowwise_df)CCAFE::vcf_sample (CollapsedVCF)CCPlotR::toy_data (tbl_df)CCPlotR::toy_exp (grouped_df)CCPROMISE::exmplESet (ExpressionSet)CCPROMISE::exmplGeneSet (GeneSetCollection)CCPROMISE::exmplMSet (ExpressionSet)CCPROMISE::exmplPat (data.frame)CDI::one_batch_matrix (matrix)CDI::one_batch_matrix_celltype (character)CDI::one_batch_matrix_label_df (data.frame)CDI::two_batch_matrix (matrix)CDI::two_batch_matrix_batch (character)CDI::two_batch_matrix_celltype (character)CDI::two_batch_matrix_label_df (data.frame)celaref::de_table.demo_query (data.frame)celaref::de_table.demo_ref (data.frame)celaref::demo_cell_info_table (data.frame)celaref::demo_counts_matrix (matrix)celaref::demo_gene_info_table (data.frame)celaref::demo_microarray_expr (matrix)celaref::demo_microarray_sample_sheet (grouped_df)celaref::demo_query_se (SummarizedExperiment)celaref::demo_ref_se (SummarizedExperiment)celda::celdaCGGridSearchRes (celdaList)celda::celdaCGMod (celda_CG)celda::celdaCGSim (list)celda::celdaCMod 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(data.frame)YAPSA::cutoffPCAWG_SBS_WGSWES_artifPid_df (data.frame)YAPSA::cutoffPCAWG_SBS_WGSWES_realPid_df (data.frame)YAPSA::exchange_colour_vector (character)YAPSA::exome_mutCatRaw_df (data.frame)YAPSA::GenomeOfNl_raw (data.frame)YAPSA::lymphoma_Nature2013_COSMIC_cutoff_exposures_df (data.frame)YAPSA::lymphoma_Nature2013_raw_df (data.frame)YAPSA::lymphoma_PID_df (data.frame)YAPSA::lymphoma_test_df (data.frame)YAPSA::lymphomaNature2013_mutCat_df (data.frame)YAPSA::MutCat_indel_df (data.frame)YAPSA::PCAWG_SP_ID_sigInd_df (data.frame)YAPSA::PCAWG_SP_ID_sigs_df (data.frame)YAPSA::PCAWG_SP_SBS_sigInd_Artif_df (data.frame)YAPSA::PCAWG_SP_SBS_sigInd_Real_df (data.frame)YAPSA::PCAWG_SP_SBS_sigs_Artif_df (data.frame)YAPSA::PCAWG_SP_SBS_sigs_Real_df (data.frame)YAPSA::rel_lymphoma_Nature2013_COSMIC_cutoff_exposures_df (data.frame)YAPSA::targetCapture_cor_factors (list)yarn::bladder (ExpressionSet)yarn::skin (ExpressionSet)zinbwave::toydata (matrix)zitools::mtx (matrix)ZygosityPredictor::GR_GENE_MODEL (GRanges)ZygosityPredictor::GR_GERM_SMALL_VARS (GRanges)ZygosityPredictor::GR_HAPLOBLOCKS (GRanges)ZygosityPredictor::GR_SCNA (GRanges)ZygosityPredictor::GR_SOM_SMALL_VARS (GRanges)

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