Man pages for GreenleafLab/ChrAccR
Analyzing chromatin accessibility data in R

addSampleAnnotCol-DsAcc-methodaddSampleAnnotCol-methods
aggregateRegionCounts-DsATAC-methodaggregateRegionCounts-methods
callPeaks-DsATAC-methodcallPeaks-methods
ChrAccRChrAccR: Analyzing chromatin accessibility data in R.
cleanMemcleanMem
collapseMotifMatrixcollapseMotifMatrix
colZscorescolZscores
computeDiffAcc.rnb.nomecomputeDiffAcc.rnb.nome
createReport_differential-DsATAC-methodcreateReport_differential-methods
createReport_exploratory-DsATAC-methodcreateReport_exploratory-methods
createReport_filtering-DsATAC-methodcreateReport_filtering-methods
createReport_normalization-DsATAC-methodcreateReport_normalization-methods
createReport_summary-DsATAC-methodcreateReport_summary-methods
dimRed_UMAP-DsATACsc-methoddimRed_UMAP-methods
DsAcc-classDsAcc
DsATAC.bamDsATAC.bam
DsATAC.cellrangerDsATAC.cellranger
DsATAC-classDsATAC
DsATAC.fragmentBedDsATAC.fragmentBed
DsATACsc.archrDsATACsc.archr
DsATACsc-classDsATACsc
DsATACsc.fragmentsDsATACsc.fragments
DsATAC.snakeATACDsATAC.snakeATAC
DsNOMe.bisSNPDsNOMe.bisSNP
DsNOMe-classDsNOMe
exportCountTracks-DsATAC-methodexportCountTracks-methods
fastqDirToTablefastqDirToTable
filterByGRanges-DsATAC-methodfilterByGRanges-methods
filterCellsTssEnrichment-DsATAC-methodfilterCellsTssEnrichment-methods
filterChroms-DsATAC-methodfilterChroms-methods
filterLowCovg-DsATAC-methodfilterLowCovg-methods
findNearestGeneForGrfindNearestGeneForGr
findOrderedNamesfindOrderedNames
getATACfragmentsgetATACfragments
getChrAccRAnnotationPackagegetChrAccRAnnotationPackage
getChromVarDev-DsATAC-methodgetChromVarDev-methods
getCiceroGeneActivities-DsATAC-methodgetCiceroGeneActivities-methods
getComparisonInfogetComparisonInfo
getComparisonTable-DsAcc-methodgetComparisonTable-methods
getConfigElementgetConfigElement
getConsensusPeakSetgetConsensusPeakSet
getCoord-DsAcc-methodgetCoord-methods
getCounts-DsATAC-methodgetCounts-methods
getCountsSE-DsATAC-methodgetCountsSE-methods
getCoverage-DsATAC-methodgetCoverage-methods
getCovg-DsNOMe-methodgetCovg-methods
getDESeq2Dataset-DsATAC-methodgetDESeq2Dataset-methods
getDiffAcc-DsATAC-methodgetDiffAcc-methods
getFragmentGr-DsATAC-methodgetFragmentGr-methods
getFragmentGrl-DsATAC-methodgetFragmentGrl-methods
getFragmentNum-DsATAC-methodgetFragmentNum-methods
getGenome-DsAcc-methodgetGenome-methods
getGenomeObjectgetGenomeObject
getGroupsFromTablegetGroupsFromTable
getInsertionKmerFreq-DsATAC-methodgetInsertionKmerFreq-methods
getInsertionSites-DsATAC-methodgetInsertionSites-methods
getJasparAnnotgetJasparAnnot
getJasparSymbolsgetJasparSymbols
getMeth-DsNOMe-methodgetMeth-methods
getMonocleCellDataSet-DsATAC-methodgetMonocleCellDataSet-methods
getMotifClusteringgetMotifClustering
getMotifDistMatgetMotifDistMat
getMotifDistMat.jaspargetMotifDistMat.jaspar
getMotifEnrichment-DsATAC-methodgetMotifEnrichment-methods
getMotifFootprints-DsATAC-methodgetMotifFootprints-methods
getMotifOccurrencesgetMotifOccurrences
getNonOverlappingByScoregetNonOverlappingByScore
getNRegions-DsAcc-methodgetNRegions-methods
getPeakSet.snakeATACgetPeakSet.snakeATAC
getQuickTssEnrichment-DsATAC-methodgetQuickTssEnrichment-methods
getRegionMapping-DsNOMe-methodgetRegionMapping-methods
getRegionTypes-DsAcc-methodgetRegionTypes-methods
getSampleAnnot-DsAcc-methodgetSampleAnnot-methods
getSampleMetrics.snakeATACgetSampleMetrics.snakeATAC
getSamples-DsAcc-methodgetSamples-methods
getScQcStatsTab-DsATACsc-methodgetScQcStatsTab-methods
getTfAnnotgetTfAnnot
getTssEnrichmentBatch-DsATAC-methodgetTssEnrichmentBatch-methods
getTssEnrichment-DsATAC-methodgetTssEnrichment-methods
hmSeqLogohmSeqLogo
isCanonicalChromisCanonicalChrom
iterativeLSI-DsATACsc-methoditerativeLSI-methods
join-DsATAC-methodjoin-methods
length-DsAcc-methodRetrieve the number of samples contained in a DsAcc object
loadConfigloadConfig
loadDsAccloadDsAcc
maskMethNA-DsNOMe-methodmaskMethNA-methods
mergePseudoBulk-DsATACsc-methodmergePseudoBulk-methods
mergeSamples-DsATAC-methodmergeSamples-methods
mergeStrands-DsNOMe-methodmergeStrands-methods
normalizeMeth-DsNOMe-methodnormalizeMeth-methods
plotInsertSizeDistribution-DsATAC-methodplotInsertSizeDistribution-methods
prepareMotifmatchrprepareMotifmatchr
projectMatrix_UMAPprojectMatrix_UMAP
PWMatrixToProbMatrixPWMatrixToProbMatrix
readMACS2peakFilereadMACS2peakFile
regionAggregation-DsATAC-methodregionAggregation-methods
regionAggregation-DsNOMe-methodregionAggregation-methods
regionSetCounts-DsATAC-methodregionSetCounts-methods
removeFragmentData-DsATAC-methodremoveFragmentData-methods
removeRegionData-DsATAC-methodremoveRegionData-methods
removeRegions-DsAcc-methodremoveRegions-methods
removeRegions-DsATAC-methodremoveRegions-methods
removeRegions-DsNOMe-methodremoveRegions-methods
removeRegionType-DsATAC-methodremoveRegionType-methods
removeSamples-DsATAC-methodremoveSamples-methods
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-DsATACsc-methodsamplePseudoBulk-methods
saveConfigsaveConfig
saveDsAccsaveDsAcc
setConfigElementsetConfigElement
sub-DsATAC-ANY-ANY-ANY-methodSubsetting DsATAC datasets by sample
transformCounts-DsATAC-methodtransformCounts-methods
unsupervisedAnalysisSc-DsATACsc-methodunsupervisedAnalysisSc-methods
GreenleafLab/ChrAccR documentation built on March 22, 2023, 11:42 p.m.