Global functions | |
---|---|
ChrAccR | Man page |
DsATAC | Source code |
DsATAC-class | Man page |
DsATAC.bam | Man page Source code |
DsATAC.cellranger | Man page Source code |
DsATAC.fragmentBed | Man page Source code |
DsATAC.snakeATAC | Man page Source code |
DsATACsc | Source code |
DsATACsc-class | Man page |
DsATACsc.archr | Man page Source code |
DsATACsc.fragments | 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 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 |
computeDeviations_altius | 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 |
dimRed_UMAP | Man page |
dimRed_UMAP,DsATACsc-method | Man page |
exportCountTracks | Man page |
exportCountTracks,DsATAC-method | Man page |
fastDelayedArrayToMatrix | Source code |
fastqDirToTable | Man page Source code |
filterByGRanges | Man page |
filterByGRanges,DsATAC-method | Man page |
filterCellsTssEnrichment | Man page |
filterCellsTssEnrichment,DsATAC-method | Man page |
filterCellsTssEnrichment,DsATACsc-method | Man page |
filterChroms | Man page |
filterChroms,DsATAC-method | Man page |
filterLowCovg | Man page |
filterLowCovg,DsATAC-method | Man page |
findNearestGeneForGr | Man page Source code |
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 |
getMotifClusterAnnot_altius | Source code |
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 |
getScQcStatsTab | Man page |
getScQcStatsTab,DsATACsc-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 |
iterativeLSI | Man page |
iterativeLSI,DsATACsc-method | Man page |
join | Man page |
join,DsATAC-method | Man page |
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 |
mergePseudoBulk | Man page |
mergePseudoBulk,DsATACsc-method | Man page |
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 |
removeRegionData | Man page |
removeRegionData,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_chromvar | 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 |
samplePseudoBulk | Man page |
samplePseudoBulk,DsATACsc-method | Man page |
saveConfig | Man page Source code |
saveDsAcc | Man page Source code |
setConfigElement | Man page Source code |
transformCounts | Man page |
transformCounts,DsATAC-method | Man page |
unsupervisedAnalysisSc | Man page |
unsupervisedAnalysisSc,DsATACsc-method | Man page |
v2l | Source code |
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