Package: ChrAccR 0.9.21

Fabian Mueller

ChrAccR: Analyzing chromatin accessibility data in R

Tools for analyzing chromatin accessibility data in R. Bulk and single-cell ATAC-seq data are supported.

Authors:Fabian Mueller [aut, cre]

ChrAccR_0.9.21.tar.gz
ChrAccR_0.9.21.zip(r-4.5)ChrAccR_0.9.21.zip(r-4.4)ChrAccR_0.9.21.zip(r-4.3)
ChrAccR_0.9.21.tgz(r-4.4-any)ChrAccR_0.9.21.tgz(r-4.3-any)
ChrAccR_0.9.21.tar.gz(r-4.5-noble)ChrAccR_0.9.21.tar.gz(r-4.4-noble)
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ChrAccR.pdf |ChrAccR.html
ChrAccR/json (API)

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

Peer review:

Bug tracker:https://github.com/greenleaflab/chraccr/issues

On CRAN:

114 exports 16 stars 1.51 score 70 dependencies

Last updated 1 years agofrom:43d010896d

Exports:addSampleAnnotColaggregateRegionCountscallPeakscleanMemcollapseMotifMatrixcolZscorescomputeDiffAcc.rnb.nomecreateReport_differentialcreateReport_exploratorycreateReport_filteringcreateReport_normalizationcreateReport_summarydimRed_UMAPDsATAC.bamDsATAC.cellrangerDsATAC.fragmentBedDsATAC.snakeATACDsATACsc.archrDsATACsc.fragmentsDsNOMe.bisSNPexportCountTracksfastqDirToTablefilterByGRangesfilterCellsTssEnrichmentfilterChromsfilterLowCovgfindGroupMarkersfindNearestGeneForGrfindOrderedNamesgetATACfragmentsgetChromVarDevgetCiceroGeneActivitiesgetComparisonInfogetComparisonTablegetConfigElementgetConsensusPeakSetgetCoordgetCountsgetCountsSEgetCoveragegetCovggetDESeq2DatasetgetDiffAccgetFragmentGrgetFragmentGrlgetFragmentNumgetGenomegetGenomeObjectgetGroupsFromTablegetInsertionKmerFreqgetInsertionSitesgetJasparAnnotgetMethgetMonocleCellDataSetgetMotifClusteringgetMotifDistMatgetMotifEnrichmentgetMotifFootprintsgetMotifOccurrencesgetNonOverlappingByScoregetNRegionsgetPeakSet.snakeATACgetQuickTssEnrichmentgetRBFGeneActivitiesgetRegionMappinggetRegionTypesgetSampleAnnotgetSampleMetrics.snakeATACgetSamplesgetScQcStatsTabgetTfAnnotgetTssEnrichmentgetTssEnrichmentBatchhmSeqLogoisCanonicalChromiterativeLSIjoinloadConfigloadDsAccmaskMethNAmergePseudoBulkmergeSamplesmergeStrandsnormalizeMethplotInsertSizeDistributionprepareMotifmatchrprojectMatrix_UMAPreadMACS2peakFileregionAggregationregionSetCountsremoveFragmentDataremoveRegionDataremoveRegionsremoveRegionTyperemoveSamplesrowZscoresrun_atacrun_atac_chromvarrun_atac_differentialrun_atac_exploratoryrun_atac_filteringrun_atac_normalizationrun_atac_peakcallingrun_atac_qcrun_atac_sc_unsupervisedsafeMatrixStatssamplePseudoBulksaveConfigsaveDsAccsetConfigElementsimulateDoubletssmoothMagictransformCountsunsupervisedAnalysisSc

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayfansifarverformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemuLogRmunsellmuRtoolsnlmeopensslpillarpkgconfigR6RColorBrewerRhtslibrlangRsamtoolsS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Subsetting DsATAC datasets by sample[,DsATAC,ANY,ANY,ANY-method
addSampleAnnotCol-methodsaddSampleAnnotCol addSampleAnnotCol,DsAcc-method
aggregateRegionCounts-methodsaggregateRegionCounts aggregateRegionCounts,DsATAC-method
callPeaks-methodscallPeaks callPeaks,DsATAC-method
ChrAccR: Analyzing chromatin accessibility data in R.ChrAccR
cleanMemcleanMem
collapseMotifMatrixcollapseMotifMatrix
colZscorescolZscores
computeDiffAcc.rnb.nomecomputeDiffAcc.rnb.nome rnb.execute.computeDiffMeth
createReport_differential-methodscreateReport_differential createReport_differential,DsATAC-method
createReport_exploratory-methodscreateReport_exploratory createReport_exploratory,DsATAC-method
createReport_filtering-methodscreateReport_filtering createReport_filtering,DsATAC-method
createReport_normalization-methodscreateReport_normalization createReport_normalization,DsATAC-method
createReport_summary-methodscreateReport_summary createReport_summary,DsATAC-method
dimRed_UMAP-methodsdimRed_UMAP dimRed_UMAP,DsATACsc-method
DsAccDsAcc-class
DsATACDsATAC-class
DsATAC.bamDsATAC.bam
DsATAC.cellrangerDsATAC.cellranger
DsATAC.fragmentBedDsATAC.fragmentBed
DsATAC.snakeATACDsATAC.snakeATAC
DsATACscDsATACsc-class
DsATACsc.archrDsATACsc.archr
DsATACsc.fragmentsDsATACsc.fragments
DsNOMeDsNOMe-class
DsNOMe.bisSNPDsNOMe.bisSNP
exportCountTracks-methodsexportCountTracks exportCountTracks,DsATAC-method
fastqDirToTablefastqDirToTable
filterByGRanges-methodsfilterByGRanges filterByGRanges,DsATAC-method
filterCellsTssEnrichment-methodsfilterCellsTssEnrichment filterCellsTssEnrichment,DsATAC-method filterCellsTssEnrichment,DsATACsc-method
filterChroms-methodsfilterChroms filterChroms,DsATAC-method
filterLowCovg-methodsfilterLowCovg filterLowCovg,DsATAC-method
findNearestGeneForGrfindNearestGeneForGr
findOrderedNamesfindOrderedNames
getATACfragmentsgetATACfragments
getChrAccRAnnotationPackagegetChrAccRAnnotationPackage
getChromVarDev-methodsgetChromVarDev getChromVarDev,DsATAC-method
getCiceroGeneActivities-methodsgetCiceroGeneActivities getCiceroGeneActivities,DsATAC-method
getComparisonInfogetComparisonInfo
getComparisonTable-methodsgetComparisonTable getComparisonTable,DsAcc-method
getConfigElementgetConfigElement
getConsensusPeakSetgetConsensusPeakSet
getCoord-methodsgetCoord getCoord,DsAcc-method
getCounts-methodsgetCounts getCounts,DsATAC-method
getCountsSE-methodsgetCountsSE getCountsSE,DsATAC-method
getCoverage-methodsgetCoverage getCoverage,DsATAC-method
getCovg-methodsgetCovg getCovg,DsNOMe-method
getDESeq2Dataset-methodsgetDESeq2Dataset getDESeq2Dataset,DsATAC-method
getDiffAcc-methodsgetDiffAcc getDiffAcc,DsATAC-method
getFragmentGr-methodsgetFragmentGr getFragmentGr,DsATAC-method
getFragmentGrl-methodsgetFragmentGrl getFragmentGrl,DsATAC-method
getFragmentNum-methodsgetFragmentNum getFragmentNum,DsATAC-method
getGenome-methodsgetGenome getGenome,DsAcc-method
getGenomeObjectgetGenomeObject
getGroupsFromTablegetGroupsFromTable
getInsertionKmerFreq-methodsgetInsertionKmerFreq getInsertionKmerFreq,DsATAC-method
getInsertionSites-methodsgetInsertionSites getInsertionSites,DsATAC-method
getJasparAnnotgetJasparAnnot
getJasparSymbolsgetJasparSymbols
getMeth-methodsgetMeth getMeth,DsNOMe-method
getMonocleCellDataSet-methodsgetMonocleCellDataSet getMonocleCellDataSet,DsATAC-method
getMotifClusteringgetMotifClustering
getMotifDistMatgetMotifDistMat
getMotifDistMat.jaspargetMotifDistMat.jaspar
getMotifEnrichment-methodsgetMotifEnrichment getMotifEnrichment,DsATAC-method
getMotifFootprints-methodsgetMotifFootprints getMotifFootprints,DsATAC-method
getMotifOccurrencesgetMotifOccurrences
getNonOverlappingByScoregetNonOverlappingByScore
getNRegions-methodsgetNRegions getNRegions,DsAcc-method
getPeakSet.snakeATACgetPeakSet.snakeATAC
getQuickTssEnrichment-methodsgetQuickTssEnrichment getQuickTssEnrichment,DsATAC-method
getRegionMapping-methodsgetRegionMapping getRegionMapping,DsNOMe-method
getRegionTypes-methodsgetRegionTypes getRegionTypes,DsAcc-method
getSampleAnnot-methodsgetSampleAnnot getSampleAnnot,DsAcc-method
getSampleMetrics.snakeATACgetSampleMetrics.snakeATAC
getSamples-methodsgetSamples getSamples,DsAcc-method
getScQcStatsTab-methodsgetScQcStatsTab getScQcStatsTab,DsATACsc-method
getTfAnnotgetTfAnnot
getTssEnrichment-methodsgetTssEnrichment getTssEnrichment,DsATAC-method
getTssEnrichmentBatch-methodsgetTssEnrichmentBatch getTssEnrichmentBatch,DsATAC-method
hmSeqLogohmSeqLogo
isCanonicalChromisCanonicalChrom
iterativeLSI-methodsiterativeLSI iterativeLSI,DsATACsc-method
join-methodsjoin join,DsATAC-method
Retrieve the number of samples contained in a DsAcc objectlength,DsAcc-method
loadConfigloadConfig
loadDsAccloadDsAcc
maskMethNA-methodsmaskMethNA maskMethNA,DsNOMe-method
mergePseudoBulk-methodsmergePseudoBulk mergePseudoBulk,DsATACsc-method
mergeSamples-methodsmergeSamples mergeSamples,DsATAC-method
mergeStrands-methodsmergeStrands mergeStrands,DsNOMe-method
normalizeMeth-methodsnormalizeMeth normalizeMeth,DsNOMe-method
plotInsertSizeDistribution-methodsplotInsertSizeDistribution plotInsertSizeDistribution,DsATAC-method
prepareMotifmatchrprepareMotifmatchr
projectMatrix_UMAPprojectMatrix_UMAP
PWMatrixToProbMatrixPWMatrixToProbMatrix
readMACS2peakFilereadMACS2peakFile
regionAggregation-methodsregionAggregation,DsATAC-method
regionAggregation-methodsregionAggregation regionAggregation,DsNOMe-method
regionSetCounts-methodsregionSetCounts regionSetCounts,DsATAC-method
removeFragmentData-methodsremoveFragmentData removeFragmentData,DsATAC-method
removeRegionData-methodsremoveRegionData removeRegionData,DsATAC-method
removeRegions-methodsremoveRegions removeRegions,DsAcc-method
removeRegions-methodsremoveRegions,DsATAC-method
removeRegions-methodsremoveRegions,DsNOMe-method
removeRegionType-methodsremoveRegionType removeRegionType,DsATAC-method
removeSamples-methodsremoveSamples removeSamples,DsATAC-method
rowZscoresrowZscores
run_atacrun_atac
run_atac_chromvarrun_atac_chromvar
run_atac_differentialrun_atac_differential
run_atac_exploratoryrun_atac_exploratory
run_atac_filteringrun_atac_filtering
run_atac_normalizationrun_atac_normalization
run_atac_peakcallingrun_atac_peakcalling
run_atac_qcrun_atac_qc
run_atac_sc_unsupervisedrun_atac_sc_unsupervised
safeMatrixStatssafeMatrixStats
samplePseudoBulk-methodssamplePseudoBulk samplePseudoBulk,DsATACsc-method
saveConfigsaveConfig
saveDsAccsaveDsAcc
setConfigElementsetConfigElement
transformCounts-methodstransformCounts transformCounts,DsATAC-method
unsupervisedAnalysisSc-methodsunsupervisedAnalysisSc unsupervisedAnalysisSc,DsATACsc-method