Package: Repitools 1.51.0
Mark Robinson
Repitools: Epigenomic tools
Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.
Authors:
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Repitools.pdf |Repitools.html✨
Repitools/json (API)
| # Install 'Repitools' in R: |
| install.packages('Repitools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- chr21genes - Positions of Genes on Human Chromosome 21
- expr - Vector of expression differences
- samplesList - Short Reads from Cancer and Normal
On BioConductor:Repitools-1.51.0(bioc 3.20)Repitools-1.50.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:62a6cd3da1
Exports:abcdDNAabsoluteCNAdjustedCopyEstimateannoDF2GRannoGR2DFannotationBlocksCountsannotationBlocksLookupannotationCountsannotationLookupBAM2GRangesBAM2GRangesListBasic_StatisticsBayMethListbinPlotsblocksblocksStatscheckProbesChromaBlockschromosomeCNplotsClusteredScoresListclusterPlotsclusterscontrolcontrol<-CopyEstimatecpgBoxplotscpgDenscpgDens<-cpgDensityCalccpgDensityPlotcutoffdetermineOffsetempBayesenrichmentCalcenrichmentPlotFDRTablefeatureBlocksfeatureScoresfindClustersfOffsetfOffset<-GCadjustCopyGCAdjustParamsGCbiasPlotsgcContentCalcgenomeBlocksgenQCgetSampleOffsetshyperg2F1_vecloadPairFileloadSampleDirectorymakeWindowLookupTablemappabilityCalcmaskEmpBayesmaskEmpBayes<-maskOutmergeReplicatesmethEstmethEst<-methylEstMismatchesMismatchTablemultiHeatmapncontrolnsampleInterestOverrepresented_sequencesPer_base_GC_contentPer_base_N_contentPer_base_sequence_contentPer_base_sequence_qualityPer_sequence_GC_contentPer_sequence_quality_scoresplotClustersplotQdnaByCNpriorTabpriorTab<-processNDFprofilePlotsQdnaDatareadFastQCregionsregionStatsrelativeCNsampleInterestsampleInterest<-Sequence_Duplication_LevelsSequence_Length_DistributionsequenceCalcsetCNVOffsetsshowsubsetRowssummarizeScorestableswindows<-writeWig
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomecaToolsclustercodetoolscpp11crayoncurlDelayedArrayDNAcopyedgeRformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgplotsgsmoothrgtoolshttrIRangesjsonliteKernSmoothlambda.rlatticelimmalocfitMASSMatrixMatrixGenericsmatrixStatsmimeopensslR6RcppRCurlrestfulrRhtslibrjsonRsamtoolsRsolnprtracklayerS4ArraysS4VectorssnowSparseArraystatmodSummarizedExperimentsystruncnormUCSC.utilsXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A wrapper for fitting the offset-adjusted ABCD-DNA GLM | abcdDNA |
| Calculate and Segment Absolute Copy Number from Sequencing Counts | absoluteCN absoluteCN,data.frame,matrix,GCAdjustParams-method absoluteCN,GRanges,matrix,GCAdjustParams-method |
| Container for results of GC adjusted copy number estimation. | AdjustedCopyEstimate AdjustedCopyEstimate,numeric,GRanges,numeric,numeric,matrix,list,matrix,character-method AdjustedCopyEstimate-class show,AdjustedCopyEstimate-method |
| Placeholder For AffymetrixCdfFile Documentation | AffymetrixCdfFile AffymetrixCdfFile-class |
| Placeholder For AffymetrixCelSet Documentation | AffymetrixCelSet AffymetrixCelSet-class |
| Convert a 'data.frame' to a 'GRanges'. | annoDF2GR annoDF2GR,data.frame-method |
| Convert an annotated 'GRanges' to a 'data.frame'. | annoGR2DF annoGR2DF,GRanges-method |
| Counts the number of sequencing reads within supplied genomic blocks. | annotationBlocksCounts annotationBlocksCounts,ANY,data.frame-method annotationBlocksCounts,character,GRanges-method annotationBlocksCounts,GRanges,GRanges-method annotationBlocksCounts,GRangesList,GRanges-method |
| Forms a mapping between probe locations and chromosomal blocks (regions). | annotationBlocksLookup annotationBlocksLookup,data.frame,data.frame-method annotationBlocksLookup,data.frame,GRanges-method |
| Counts the number of sequencing reads surrounding supplied annotations | annotationCounts annotationCounts,ANY,data.frame-method annotationCounts,ANY,GRanges-method |
| Forms a mapping between probes on a tiling array and windows surrounding the TSSs of genes. | annotationLookup annotationLookup,data.frame,data.frame-method annotationLookup,data.frame,GRanges-method |
| Read in a (list of) BAM file(s) into a GRanges(List) object. | BAM2GRanges BAM2GRanges,character-method BAM2GRangesList BAM2GRangesList,character-method |
| Class '"BayMethList"' | BayMethList BayMethList,GRanges,matrix,matrix,numeric-method BayMethList-class control control,BayMethList-method control<- control<-,BayMethList-method cpgDens cpgDens,BayMethList-method cpgDens<- cpgDens<-,BayMethList-method fOffset fOffset,BayMethList-method fOffset<- fOffset<-,BayMethList-method length length,BayMethList-method maskEmpBayes maskEmpBayes,BayMethList-method maskEmpBayes<- maskEmpBayes<-,BayMethList-method methEst methEst,BayMethList-method methEst<- methEst<-,BayMethList-method ncontrol ncontrol,BayMethList-method nsampleInterest nsampleInterest,BayMethList-method priorTab priorTab,BayMethList-method priorTab<- priorTab<-,BayMethList-method sampleInterest sampleInterest,BayMethList-method sampleInterest<- sampleInterest<-,BayMethList-method show,BayMethList-method windows windows,BayMethList-method windows<- windows<-,BayMethList-method [,BayMethList,ANY,missing,ANY-method |
| Create line plots of averaged signal across a promoter | binPlots binPlots,ScoresList-method |
| Calculate statistics for regions in the genome | blocksStats blocksStats,ANY,data.frame-method blocksStats,ANY,GRanges-method |
| Check Probe Specificity for Some Regions | checkProbes checkProbes,data.frame,data.frame-method checkProbes,GRanges,GRanges-method |
| Positions of Genes on Human Chromosome 21 | chr21genes |
| A function to find areas of enrichment in sequencing data | ChromaBlocks ChromaBlocks,GRangesList,GRangesList-method |
| ChromaResults class | blocks blocks,ChromaResults-method ChromaResults ChromaResults-class class:ChromaResults cutoff cutoff,ChromaResults-method FDRTable FDRTable,ChromaResults-method regions regions,ChromaResults-method show,ChromaResults-method |
| Plot copy number by chromosome | chromosomeCNplots chromosomeCNplots,AdjustedCopyEstimate-method chromosomeCNplots,CopyEstimate-method |
| Container for coverage matrices with clustering results. | ClusteredScoresList ClusteredScoresList,ScoresList-method ClusteredScoresList-class clusters clusters,ClusteredScoresList-method show,ClusteredScoresList-method subsetRows,ClusteredScoresList-method [,ClusteredScoresList,ANY,missing,ANY-method |
| Visualisation of tables of feature coverages. | clusterPlots clusterPlots,ClusteredScoresList-method clusterPlots,ScoresList-method |
| Container for results of fold change copy number estimation. | CopyEstimate CopyEstimate,GRanges,matrix,GRangesList,character-method CopyEstimate-class show,CopyEstimate-method |
| Boxplots of intensity, binned by Cpg Density | cpgBoxplots cpgBoxplots,AffymetrixCelSet-method cpgBoxplots,matrix-method |
| Calculate CpG Density in a Window | cpgDensityCalc cpgDensityCalc,data.frame,BSgenome-method cpgDensityCalc,GRanges,BSgenome-method cpgDensityCalc,GRangesList,BSgenome-method |
| Plot the distribution of sequencing reads CpG densities. | cpgDensityPlot cpgDensityPlot,GRangesList-method |
| Function to determine the normalising offset f that accounts for the relative sequencing depth. | determineOffset |
| Function to calculate prior parameters using empirical Bayes. | empBayes |
| Calculate sequencing enrichment | enrichmentCalc enrichmentCalc,GRanges-method enrichmentCalc,GRangesList-method |
| Plot the distribution of sequencing enrichment. | enrichmentPlot enrichmentPlot,GRangesList-method |
| Vector of expression differences | expr |
| FastQC and associated classes | Basic_Statistics Basic_Statistics,FastQC-method Basic_Statistics,SequenceQC-method Basic_Statistics,SequenceQCSet-method class:FastQC class:SequenceQC class:SequenceQCSet FastQC-class Mismatches Mismatches,SequenceQC-method Mismatches,SequenceQCSet-method MismatchTable MismatchTable,SequenceQC-method MismatchTable,SequenceQCSet-method Overrepresented_sequences Overrepresented_sequences,FastQC-method Overrepresented_sequences,SequenceQC-method Overrepresented_sequences,SequenceQCSet-method Per_base_GC_content Per_base_GC_content,FastQC-method Per_base_GC_content,SequenceQC-method Per_base_GC_content,SequenceQCSet-method Per_base_N_content Per_base_N_content,FastQC-method Per_base_N_content,SequenceQC-method Per_base_N_content,SequenceQCSet-method Per_base_sequence_content Per_base_sequence_content,FastQC-method Per_base_sequence_content,SequenceQC-method Per_base_sequence_content,SequenceQCSet-method Per_base_sequence_quality Per_base_sequence_quality,FastQC-method Per_base_sequence_quality,SequenceQC-method Per_base_sequence_quality,SequenceQCSet-method Per_sequence_GC_content Per_sequence_GC_content,FastQC-method Per_sequence_GC_content,SequenceQC-method Per_sequence_GC_content,SequenceQCSet-method Per_sequence_quality_scores Per_sequence_quality_scores,FastQC-method Per_sequence_quality_scores,SequenceQC-method Per_sequence_quality_scores,SequenceQCSet-method readFastQC SequenceQC-class SequenceQCSet SequenceQCSet-class Sequence_Duplication_Levels Sequence_Duplication_Levels,FastQC-method Sequence_Duplication_Levels,SequenceQC-method Sequence_Duplication_Levels,SequenceQCSet-method Sequence_Length_Distribution Sequence_Length_Distribution,FastQC-method Sequence_Length_Distribution,SequenceQC-method Sequence_Length_Distribution,SequenceQCSet-method show,FastQC-method show,SequenceQC-method show,SequenceQCSet-method [,SequenceQCSet,ANY,missing,ANY-method |
| Make windows for distances around a reference point. | featureBlocks featureBlocks,data.frame-method featureBlocks,GRanges-method |
| Get scores at regular sample points around genomic features. | featureScores featureScores,ANY,data.frame-method featureScores,ANY,GRanges-method |
| Find Clusters Epigenetically Modified Genes | findClusters |
| Calculate Absolute Copy Number from Sequencing Counts | GCadjustCopy GCadjustCopy,data.frame,matrix,GCAdjustParams-method GCadjustCopy,GRanges,matrix,GCAdjustParams-method |
| Container for parameters for mappability and GC content adjusted absolute copy number estimation. | GCAdjustParams GCAdjustParams,BSgenome,MappabilitySource-method GCAdjustParams-class |
| Plot GC content vs. Read Counts Before Normalising, and GC content vs. Copy Estimates After Normalising. | GCbiasPlots GCbiasPlots,AdjustedCopyEstimate-method |
| Calculate The gcContent of a Region | gcContentCalc gcContentCalc,data.frame,BSgenome-method gcContentCalc,GRanges,BSgenome-method |
| Creates bins across a genome. | genomeBlocks genomeBlocks,BSgenome-method genomeBlocks,numeric-method |
| Plot Quality Checking Information for Sequencing Data | genQC genQC,character-method genQC,SequenceQCSet-method |
| Translate Affymetrix probe information in a table. | getProbePositionsDf getProbePositionsDf,AffymetrixCdfFile-method |
| Calculates the sample-specific offsets, using the neutral state | getSampleOffsets |
| Masking files for hg19 | hcRegions |
| Gaussian hypergeometric function for vectorial arguments | hyperg2F1_vec |
| A routine to read Nimblegen tiling array intensities | loadPairFile |
| A routine to read Nimblegen tiling array intensities | loadSampleDirectory |
| Using the output of 'annotationLookup', create a tabular storage of the indices | makeWindowLookupTable |
| Calculate The Mappability of a Region | mappabilityCalc mappabilityCalc,data.frame,MappabilitySource-method mappabilityCalc,GRanges,MappabilitySource-method |
| Superclass for datatypes that can refer to genome mappability data. | MappabilitySource MappabilitySource-class |
| Function to mask suspicious regions. | maskOut |
| Merge GRanges that are of replicate experiments. | mergeReplicates mergeReplicates,GRangesList-method |
| Function to derive regional methylation estimates. | methylEst |
| Superfigure plots | multiHeatmap |
| Plot Scores of Cluster Regions | plotClusters plotClusters,data.frame-method plotClusters,GRanges-method |
| Plotting the response of qDNA-seq data by CNV | plotQdnaByCN |
| Reads in a Nimblegen microarray design file (NDF) | processNDF |
| Create line plots of averaged signal across a promoter for gene sets, compared to random sampling. | profilePlots profilePlots,ScoresList-method |
| A container for quantitative DNA sequencing data for ABCD-DNA analyses | class:QdnaData QdnaData QdnaData-class show,QdnaData-method |
| Find Regions of significance in microarray data | class:RegionStats regionStats regionStats,AffymetrixCelSet-method regionStats,matrix-method RegionStats-class show,RegionStats-method |
| Calculate and Segment Relative Copy Number From Sequencing Counts | relativeCN relativeCN,data.frame,matrix-method relativeCN,GRanges,matrix-method |
| Short Reads from Cancer and Normal | samplesList |
| Container for 'featureScores()' output. | length,ScoresList-method names,ScoresList-method names<-,ScoresList-method ScoresList ScoresList-class show,ScoresList-method subsetRows subsetRows,ScoresList-method tables tables,ScoresList-method [,ScoresList,ANY,missing,ANY-method |
| Find occurences of a DNA pattern | sequenceCalc sequenceCalc,data.frame,BSgenome-method sequenceCalc,GRanges,BSgenome-method |
| Set the CNVOffsets of a 'QdnaData' object | setCNVOffsets |
| Subtract scores of different samples. | summarizeScores summarizeScores,ScoresList,matrix-method |
| Writes sequencing data out into wiggle files | writeWig writeWig,AffymetrixCelSet-method writeWig,GRangesList-method |
