Package: ChrAccR 0.9.21
![](https://r-universe.dev/static/nobody.jpg)
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:
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)
ChrAccR_0.9.21.tgz(r-4.4-emscripten)ChrAccR_0.9.21.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/greenleaflab/chraccr/issues
Last updated 1 years agofrom:43d010896d. Checks:ERROR: 1 WARNING: 6. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | FAIL | Aug 27 2024 |
R-4.5-win | WARNING | Aug 27 2024 |
R-4.5-linux | WARNING | Aug 27 2024 |
R-4.4-win | WARNING | Aug 27 2024 |
R-4.4-mac | WARNING | Aug 27 2024 |
R-4.3-win | WARNING | Aug 27 2024 |
R-4.3-mac | WARNING | Aug 27 2024 |
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 page | Topics |
---|---|
Subsetting DsATAC datasets by sample | [,DsATAC,ANY,ANY,ANY-method |
addSampleAnnotCol-methods | addSampleAnnotCol addSampleAnnotCol,DsAcc-method |
aggregateRegionCounts-methods | aggregateRegionCounts aggregateRegionCounts,DsATAC-method |
callPeaks-methods | callPeaks callPeaks,DsATAC-method |
ChrAccR: Analyzing chromatin accessibility data in R. | ChrAccR |
cleanMem | cleanMem |
collapseMotifMatrix | collapseMotifMatrix |
colZscores | colZscores |
computeDiffAcc.rnb.nome | computeDiffAcc.rnb.nome rnb.execute.computeDiffMeth |
createReport_differential-methods | createReport_differential createReport_differential,DsATAC-method |
createReport_exploratory-methods | createReport_exploratory createReport_exploratory,DsATAC-method |
createReport_filtering-methods | createReport_filtering createReport_filtering,DsATAC-method |
createReport_normalization-methods | createReport_normalization createReport_normalization,DsATAC-method |
createReport_summary-methods | createReport_summary createReport_summary,DsATAC-method |
dimRed_UMAP-methods | dimRed_UMAP dimRed_UMAP,DsATACsc-method |
DsAcc | DsAcc-class |
DsATAC | DsATAC-class |
DsATAC.bam | DsATAC.bam |
DsATAC.cellranger | DsATAC.cellranger |
DsATAC.fragmentBed | DsATAC.fragmentBed |
DsATAC.snakeATAC | DsATAC.snakeATAC |
DsATACsc | DsATACsc-class |
DsATACsc.archr | DsATACsc.archr |
DsATACsc.fragments | DsATACsc.fragments |
DsNOMe | DsNOMe-class |
DsNOMe.bisSNP | DsNOMe.bisSNP |
exportCountTracks-methods | exportCountTracks exportCountTracks,DsATAC-method |
fastqDirToTable | fastqDirToTable |
filterByGRanges-methods | filterByGRanges filterByGRanges,DsATAC-method |
filterCellsTssEnrichment-methods | filterCellsTssEnrichment filterCellsTssEnrichment,DsATAC-method filterCellsTssEnrichment,DsATACsc-method |
filterChroms-methods | filterChroms filterChroms,DsATAC-method |
filterLowCovg-methods | filterLowCovg filterLowCovg,DsATAC-method |
findNearestGeneForGr | findNearestGeneForGr |
findOrderedNames | findOrderedNames |
getATACfragments | getATACfragments |
getChrAccRAnnotationPackage | getChrAccRAnnotationPackage |
getChromVarDev-methods | getChromVarDev getChromVarDev,DsATAC-method |
getCiceroGeneActivities-methods | getCiceroGeneActivities getCiceroGeneActivities,DsATAC-method |
getComparisonInfo | getComparisonInfo |
getComparisonTable-methods | getComparisonTable getComparisonTable,DsAcc-method |
getConfigElement | getConfigElement |
getConsensusPeakSet | getConsensusPeakSet |
getCoord-methods | getCoord getCoord,DsAcc-method |
getCounts-methods | getCounts getCounts,DsATAC-method |
getCountsSE-methods | getCountsSE getCountsSE,DsATAC-method |
getCoverage-methods | getCoverage getCoverage,DsATAC-method |
getCovg-methods | getCovg getCovg,DsNOMe-method |
getDESeq2Dataset-methods | getDESeq2Dataset getDESeq2Dataset,DsATAC-method |
getDiffAcc-methods | getDiffAcc getDiffAcc,DsATAC-method |
getFragmentGr-methods | getFragmentGr getFragmentGr,DsATAC-method |
getFragmentGrl-methods | getFragmentGrl getFragmentGrl,DsATAC-method |
getFragmentNum-methods | getFragmentNum getFragmentNum,DsATAC-method |
getGenome-methods | getGenome getGenome,DsAcc-method |
getGenomeObject | getGenomeObject |
getGroupsFromTable | getGroupsFromTable |
getInsertionKmerFreq-methods | getInsertionKmerFreq getInsertionKmerFreq,DsATAC-method |
getInsertionSites-methods | getInsertionSites getInsertionSites,DsATAC-method |
getJasparAnnot | getJasparAnnot |
getJasparSymbols | getJasparSymbols |
getMeth-methods | getMeth getMeth,DsNOMe-method |
getMonocleCellDataSet-methods | getMonocleCellDataSet getMonocleCellDataSet,DsATAC-method |
getMotifClustering | getMotifClustering |
getMotifDistMat | getMotifDistMat |
getMotifDistMat.jaspar | getMotifDistMat.jaspar |
getMotifEnrichment-methods | getMotifEnrichment getMotifEnrichment,DsATAC-method |
getMotifFootprints-methods | getMotifFootprints getMotifFootprints,DsATAC-method |
getMotifOccurrences | getMotifOccurrences |
getNonOverlappingByScore | getNonOverlappingByScore |
getNRegions-methods | getNRegions getNRegions,DsAcc-method |
getPeakSet.snakeATAC | getPeakSet.snakeATAC |
getQuickTssEnrichment-methods | getQuickTssEnrichment getQuickTssEnrichment,DsATAC-method |
getRegionMapping-methods | getRegionMapping getRegionMapping,DsNOMe-method |
getRegionTypes-methods | getRegionTypes getRegionTypes,DsAcc-method |
getSampleAnnot-methods | getSampleAnnot getSampleAnnot,DsAcc-method |
getSampleMetrics.snakeATAC | getSampleMetrics.snakeATAC |
getSamples-methods | getSamples getSamples,DsAcc-method |
getScQcStatsTab-methods | getScQcStatsTab getScQcStatsTab,DsATACsc-method |
getTfAnnot | getTfAnnot |
getTssEnrichment-methods | getTssEnrichment getTssEnrichment,DsATAC-method |
getTssEnrichmentBatch-methods | getTssEnrichmentBatch getTssEnrichmentBatch,DsATAC-method |
hmSeqLogo | hmSeqLogo |
isCanonicalChrom | isCanonicalChrom |
iterativeLSI-methods | iterativeLSI iterativeLSI,DsATACsc-method |
join-methods | join join,DsATAC-method |
Retrieve the number of samples contained in a DsAcc object | length,DsAcc-method |
loadConfig | loadConfig |
loadDsAcc | loadDsAcc |
maskMethNA-methods | maskMethNA maskMethNA,DsNOMe-method |
mergePseudoBulk-methods | mergePseudoBulk mergePseudoBulk,DsATACsc-method |
mergeSamples-methods | mergeSamples mergeSamples,DsATAC-method |
mergeStrands-methods | mergeStrands mergeStrands,DsNOMe-method |
normalizeMeth-methods | normalizeMeth normalizeMeth,DsNOMe-method |
plotInsertSizeDistribution-methods | plotInsertSizeDistribution plotInsertSizeDistribution,DsATAC-method |
prepareMotifmatchr | prepareMotifmatchr |
projectMatrix_UMAP | projectMatrix_UMAP |
PWMatrixToProbMatrix | PWMatrixToProbMatrix |
readMACS2peakFile | readMACS2peakFile |
regionAggregation-methods | regionAggregation,DsATAC-method |
regionAggregation-methods | regionAggregation regionAggregation,DsNOMe-method |
regionSetCounts-methods | regionSetCounts regionSetCounts,DsATAC-method |
removeFragmentData-methods | removeFragmentData removeFragmentData,DsATAC-method |
removeRegionData-methods | removeRegionData removeRegionData,DsATAC-method |
removeRegions-methods | removeRegions removeRegions,DsAcc-method |
removeRegions-methods | removeRegions,DsATAC-method |
removeRegions-methods | removeRegions,DsNOMe-method |
removeRegionType-methods | removeRegionType removeRegionType,DsATAC-method |
removeSamples-methods | removeSamples removeSamples,DsATAC-method |
rowZscores | rowZscores |
run_atac | run_atac |
run_atac_chromvar | run_atac_chromvar |
run_atac_differential | run_atac_differential |
run_atac_exploratory | run_atac_exploratory |
run_atac_filtering | run_atac_filtering |
run_atac_normalization | run_atac_normalization |
run_atac_peakcalling | run_atac_peakcalling |
run_atac_qc | run_atac_qc |
run_atac_sc_unsupervised | run_atac_sc_unsupervised |
safeMatrixStats | safeMatrixStats |
samplePseudoBulk-methods | samplePseudoBulk samplePseudoBulk,DsATACsc-method |
saveConfig | saveConfig |
saveDsAcc | saveDsAcc |
setConfigElement | setConfigElement |
transformCounts-methods | transformCounts transformCounts,DsATAC-method |
unsupervisedAnalysisSc-methods | unsupervisedAnalysisSc unsupervisedAnalysisSc,DsATACsc-method |