API for GreenleafLab/ChrAccR
Analyzing chromatin accessibility data in R

Global functions
ChrAccR Man page
DsATAC Source code
DsATAC-class Man page
DsATAC.bam Man page Source code
DsATAC.fragmentBed Man page Source code
DsATAC.snakeATAC Man page Source code
DsAcc Source code
DsAcc-class Man page
DsNOMe Source code
DsNOMe-class Man page
DsNOMe.bisSNP Man page Source code
FUN Source code Source code Source code Source code Source code Source code Source code Source code Source code Source code
PWMatrixToProbMatrix Man page Source code
[,DsATAC,ANY,ANY,ANY-method Man page
addSampleAnnotCol Man page
addSampleAnnotCol,DsAcc-method Man page
aggregateRegionCounts Man page
aggregateRegionCounts,DsATAC-method Man page
callPeaks Man page
callPeaks,DsATAC-method Man page
cleanMem Man page Source code
colZscores Man page Source code
collapseMotifMatrix Man page Source code
computeDiffAcc.rnb.nome Man page Source code
computeDiffAcc.rnb.nome.bin.region Source code
createReport_differential Man page
createReport_differential,DsATAC-method Man page
createReport_exploratory Man page
createReport_exploratory,DsATAC-method Man page
createReport_filtering Man page
createReport_filtering,DsATAC-method Man page
createReport_normalization Man page
createReport_normalization,DsATAC-method Man page
createReport_summary Man page
createReport_summary,DsATAC-method Man page
custom_cicero_cds Source code
exportCountTracks Man page
exportCountTracks,DsATAC-method Man page
fastDelayedArrayToMatrix Source code
fastqDirToTable Man page Source code
filterByGRanges Man page
filterByGRanges,DsATAC-method Man page
filterChroms Man page
filterChroms,DsATAC-method Man page
filterLowCovg Man page
filterLowCovg,DsATAC-method Man page
findOrderedNames Man page Source code
getATACfragments Man page Source code
getChrAccRAnnotationPackage Man page Source code
getChromVarDev Man page
getChromVarDev,DsATAC-method Man page
getCiceroGeneActivities Man page
getCiceroGeneActivities,DsATAC-method Man page
getComparisonInfo Man page Source code
getComparisonTable Man page
getComparisonTable,DsAcc-method Man page
getConfigElement Man page Source code
getConsensusPeakSet Man page Source code
getCoord Man page
getCoord,DsAcc-method Man page
getCounts Man page
getCounts,DsATAC-method Man page
getCountsSE Man page
getCountsSE,DsATAC-method Man page
getCoverage Man page
getCoverage,DsATAC-method Man page
getCovg Man page
getCovg,DsNOMe-method Man page
getDESeq2Dataset Man page
getDESeq2Dataset,DsATAC-method Man page
getDiffAcc Man page
getDiffAcc,DsATAC-method Man page
getFragmentGr Man page
getFragmentGr,DsATAC-method Man page
getFragmentGrl Man page
getFragmentGrl,DsATAC-method Man page
getFragmentNum Man page
getFragmentNum,DsATAC-method Man page
getGenome Man page
getGenome,DsAcc-method Man page
getGenomeObject Man page Source code
getGroupsFromTable Man page Source code
getInsertionKmerFreq Man page
getInsertionKmerFreq,DsATAC-method Man page
getInsertionSites Man page
getInsertionSites,DsATAC-method Man page
getInsertionSitesFromFragmentGr Source code
getJasparAnnot Man page Source code
getJasparSymbols Man page Source code
getMeth Man page
getMeth,DsNOMe-method Man page
getMonocleCellDataSet Man page
getMonocleCellDataSet,DsATAC-method Man page
getMotifClustering Man page Source code
getMotifDistMat Man page Source code
getMotifDistMat.jaspar Man page Source code
getMotifEnrichment Man page
getMotifEnrichment,DsATAC-method Man page
getMotifFootprints Man page
getMotifFootprints,DsATAC-method Man page
getMotifOccurrences Man page Source code
getNRegions Man page
getNRegions,DsAcc-method Man page
getNonOverlappingByScore Man page Source code
getPeakSet.snakeATAC Man page Source code
getQuickTssEnrichment Man page
getQuickTssEnrichment,DsATAC-method Man page
getRBF Source code
getRegionMapping Man page
getRegionMapping,DsNOMe-method Man page
getRegionTypes Man page
getRegionTypes,DsAcc-method Man page
getSampleAnnot Man page
getSampleAnnot,DsAcc-method Man page
getSampleMetrics.snakeATAC Man page Source code
getSamples Man page
getSamples,DsAcc-method Man page
getTfAnnot Man page Source code
getTssEnrichment Man page
getTssEnrichment,DsATAC-method Man page
getTssEnrichmentBatch Man page
getTssEnrichmentBatch,DsATAC-method Man page
getWfState Source code
hmSeqLogo Man page Source code
isCanonicalChrom Man page Source code
l2v Source code
length,DsAcc-method Man page
loadConfig Man page Source code
loadDsAcc Man page Source code
makeReportIndex Source code
maskMethNA Man page
maskMethNA,DsNOMe-method Man page
mergeBisSNPMethCalls Source code
mergeSamples Man page
mergeSamples,DsATAC-method Man page
mergeStrands Man page
mergeStrands,DsNOMe-method Man page
normalizeMeth Man page
normalizeMeth,DsNOMe-method Man page
permutePWMatrix Source code
permutePWMatrixList Source code
plotFootprint Source code
plotInsertSizeDistribution Man page
plotInsertSizeDistribution,DsATAC-method Man page
prepAnaDir Source code
prepareMotifmatchr Man page Source code
projectMatrix_UMAP Man page
readMACS2peakFile Man page Source code
regionAggregation Man page
regionAggregation,DsATAC-method Man page
regionAggregation,DsNOMe-method Man page
regionSetCounts Man page
regionSetCounts,DsATAC-method Man page
removeFragmentData Man page
removeFragmentData,DsATAC-method Man page
removeRegionType Man page
removeRegionType,DsATAC-method Man page
removeRegions Man page
removeRegions,DsATAC-method Man page
removeRegions,DsAcc-method Man page
removeRegions,DsNOMe-method Man page
removeSamples Man page
removeSamples,DsATAC-method Man page
resetWfToStage Source code
rmDepthPcs Source code
rnb.execute.computeDiffMeth Man page
rowZscores Man page Source code
run_atac Man page Source code
run_atac_differential Man page Source code
run_atac_exploratory Man page Source code
run_atac_filtering Man page Source code
run_atac_normalization Man page Source code
run_atac_peakcalling Man page Source code
run_atac_qc Man page Source code
run_atac_sc_unsupervised Man page Source code
safeMatrixStats Man page Source code
saveConfig Man page Source code
saveDsAcc Man page Source code
setConfigElement Man page Source code
transformCounts Man page
transformCounts,DsATAC-method Man page
v2l Source code
GreenleafLab/ChrAccR documentation built on April 28, 2020, 1:55 a.m.