Package: chromVAR 1.29.0

Alicia Schep

chromVAR: Chromatin Variation Across Regions

Determine variation in chromatin accessibility across sets of annotations or peaks. Designed primarily for single-cell or sparse chromatin accessibility data, e.g. from scATAC-seq or sparse bulk ATAC or DNAse-seq experiments.

Authors:Alicia Schep [aut, cre], Jason Buenrostro [ctb], Caleb Lareau [ctb], William Greenleaf [ths], Stanford University [cph]

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chromVAR.pdf |chromVAR.html✨
chromVAR/json (API)
NEWS

# Install 'chromVAR' in R:
install.packages('chromVAR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:chromVAR-1.27.0(bioc 3.20)chromVAR-1.26.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

singlecellsequencinggeneregulationimmunooncology

6.29 score 748 scripts 2.6k downloads 44 exports 152 dependencies

Last updated 23 days agofrom:261e3b9e02. Checks:OK: 1 NOTE: 7 ERROR: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-win-x86_64NOTEOct 30 2024
R-4.5-linux-x86_64NOTEOct 30 2024
R-4.4-win-x86_64NOTEOct 30 2024
R-4.4-mac-x86_64NOTEOct 30 2024
R-4.4-mac-aarch64NOTEOct 30 2024
R-4.3-win-x86_64NOTEOct 30 2024
R-4.3-mac-x86_64NOTEOct 30 2024
R-4.3-mac-aarch64ERROROct 30 2024

Exports:addGCBiasannotationMatchesannotationMatches<-assembleKmerscbindchromVAR_themecomputeDeviationscomputeExpectationscomputeVariabilitycountscounts<-deviationsdeviationScoresdeviationsCovariabilitydeviationsTsnedifferentialDeviationsdifferentialVariabilityfilterPeaksfilterSamplesfilterSamplesPlotgetAnnotationCorrelationgetAnnotationsgetAnnotationSynergygetBackgroundPeaksgetCisGroupsgetCountsgetFragmentsPerPeakgetFragmentsPerSamplegetJasparMotifsgetPeaksgetPermutedDatagetSampleCorrelationgetSampleDepthsgetSampleDistancegetTotalFragmentsmakeBiasBinsmakePermutedSetsmatchKmersplotDeviationsTsneplotKmerMismatchplotVariabilitypwmDistancerbindreadNarrowpeaks

Dependencies:abindannotateAnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibcachemcaToolsclicliprCNErcodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestDirichletMultinomialdplyrDTevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2glueGO.dbgtablegtoolshighrhmshtmltoolshtmlwidgetshttpuvhttrIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnabornlmeopensslpillarpkgconfigplogrplotlyplyrpngpoweRlawpracmaprettyunitsprogresspromisespurrrpwalignR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreadrreshape2restfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerRtsneS4ArraysS4VectorssassscalesseqLogoshinysnowsourcetoolsSparseArraystringistringrSummarizedExperimentsysTFBSToolsTFMPvaluetibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLxtableXVectoryamlzlibbioc

chromVAR

Alicia Schep

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2017-10-16
Started: 2017-02-07

Readme and manuals

Help Manual

Help pageTopics
addGCBiasaddGCBias addGCBias,RangedSummarizedExperiment-method addGCBias,SummarizedExperiment-method
annotationMatchesannoation_matches<-,SummarizedExperiment-method annotationMatches annotationMatches,SummarizedExperiment-method annotationMatches<- annotationMatches<-,SummarizedExperiment-method
assembleKmersassembleKmers
cbind method for chromVARDeviationscbind,chromVARDeviations-method
chromVAR: A package for computing variability across sets of peaks.chromVAR-package chromVAR
chromVAR_themechromVAR_theme
chromVARDeviationschromVARDeviations-class
computeDeviationscomputeDeviations computeDeviations,MatrixOrmatrix,list-method computeDeviations,MatrixOrmatrix,MatrixOrmatrix-method computeDeviations,MatrixOrmatrix,missingOrNULL-method computeDeviations,MatrixOrmatrix,SummarizedExperiment-method computeDeviations,SummarizedExperiment,list-method computeDeviations,SummarizedExperiment,MatrixOrmatrix-method computeDeviations,SummarizedExperiment,missingOrNULL-method computeDeviations,SummarizedExperiment,SummarizedExperiment-method
computeExpectationscomputeExpectations computeExpectations,MatrixOrmatrix-method computeExpectations,SummarizedExperiment-method
computeVariabilitycomputeVariability
Accessors for the 'counts' slot of a SummarizedExperimentcounts,SummarizedExperiment-method counts<-,SummarizedExperiment,MatrixOrmatrix-method counts<-,SummarizedExperiment-method
deviationsdeviations deviations,chromVARDeviations-method
deviationScoresdeviationScores deviationScores,chromVARDeviations-method
deviationsCovariabilitydeviationsCovariability
deviationsTsnedeviationsTsne
differentialDeviationsdifferentialDeviations
differentialVariabilitydifferentialVariability
example_countsexample_counts
filterPeaksfilterPeaks
filterSamplesfilterSamples
filterSamplesPlotfilterSamplesPlot
getAnnotationCorrelationgetAnnotationCorrelation getAnnotationCorrelation,MatrixOrmatrix,list-method getAnnotationCorrelation,MatrixOrmatrix,MatrixOrmatrix-method getAnnotationCorrelation,MatrixOrmatrix,SummarizedExperiment-method getAnnotationCorrelation,SummarizedExperiment,list-method getAnnotationCorrelation,SummarizedExperiment,MatrixOrmatrix-method getAnnotationCorrelation,SummarizedExperiment,SummarizedExperiment-method
getAnnotationsgetAnnotations getAnnotations,character-method getAnnotations,data.frame-method getAnnotations,GRangesList-method getAnnotations,list-method getAnnotations,MatrixOrmatrix-method
getAnnotationSynergygetAnnotationSynergy getAnnotationSynergy,MatrixOrmatrix,list-method getAnnotationSynergy,MatrixOrmatrix,MatrixOrmatrix-method getAnnotationSynergy,MatrixOrmatrix,SummarizedExperiment-method getAnnotationSynergy,SummarizedExperiment,list-method getAnnotationSynergy,SummarizedExperiment,MatrixOrmatrix-method getAnnotationSynergy,SummarizedExperiment,SummarizedExperiment-method
getBackgroundPeaksgetBackgroundPeaks getBackgroundPeaks,MatrixOrmatrix-method getBackgroundPeaks,RangedSummarizedExperiment-method getBackgroundPeaks,SummarizedExperiment-method
getCisGroupsgetCisGroups getCisGroups,GenomicRanges-method getCisGroups,RangedSummarizedExperiment-method
getCountsgetCounts
getFragmentsPerPeakgetFragmentsPerPeak getFragmentsPerPeak,MatrixOrmatrix-method getFragmentsPerPeak,SummarizedExperiment-method
getFragmentsPerSamplegetFragmentsPerSample getFragmentsPerSample,MatrixOrmatrix-method getFragmentsPerSample,SummarizedExperiment-method
getJasparMotifsgetJasparMotifs
getPeaksgetPeaks
getPermutedDatagetPermutedData
getSampleCorrelationgetSampleCorrelation
getSampleDepthsgetSampleDepths
getSampleDistancegetSampleDistance
getTotalFragmentsgetTotalFragments getTotalFragments,MatrixOrmatrix-method getTotalFragments,SummarizedExperiment-method
makeBiasBinsmakeBiasBins makeBiasBins,MatrixOrmatrix-method makeBiasBins,RangedSummarizedExperiment-method makeBiasBins,SummarizedExperiment-method
makePermutedSetsmakePermutedSets makePermutedSets,MatrixOrmatrix,list-method makePermutedSets,MatrixOrmatrix,MatrixOrmatrix-method makePermutedSets,MatrixOrmatrix,SummarizedExperiment-method makePermutedSets,RangedSummarizedExperiment,list-method makePermutedSets,RangedSummarizedExperiment,MatrixOrmatrix-method makePermutedSets,RangedSummarizedExperiment,SummarizedExperiment-method makePermutedSets,SummarizedExperiment,list-method makePermutedSets,SummarizedExperiment,MatrixOrmatrix-method makePermutedSets,SummarizedExperiment,SummarizedExperiment-method
matchKmersmatchKmers matchKmers,character,character-method matchKmers,character,DNAString-method matchKmers,character,DNAStringSet-method matchKmers,character,GenomicRanges-method matchKmers,character,RangedSummarizedExperiment-method matchKmers,DNAString,ANY-method matchKmers,DNAStringSet,ANY-method matchKmers,numeric,ANY-method
mini_countsmini_counts
mini_devmini_dev
mini_ixmini_ix
plotDeviationsTsneplotDeviationsTsne
plotKmerMismatchplotKmerMismatch
plotVariabilityplotVariability
pwmDistancepwmDistance
rbind method chromVARDeviationsrbind,chromVARDeviations-method
readNarrowpeaksreadNarrowpeaks