Files in GreenleafLab/ChrAccR
Analyzing chromatin accessibility data in R
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/ChrAccR.R
R/DsATAC-class.R
R/DsATACsc-class.R
R/DsAcc-class.R
R/DsNOMe-class.R
R/annotation.R
R/classDefs.R
R/config.R
R/differential.R
R/differential_nome.R
R/importTools_nome.R
R/import_atac.R
R/import_atac_10x.R
R/import_atac_archr.R
R/report_atac_differential.R
R/report_atac_exploratory.R
R/report_atac_filtering.R
R/report_atac_normalization.R
R/report_atac_summary.R
R/utils.R
R/utils_atac.R
R/utils_chromVAR.R
R/utils_filehandling.R
R/utils_motifs.R
R/workflow.R
README.md
_pkgdown.yml
inst/extdata/chraccr_logo.png
inst/extdata/dna.png
inst/extdata/motifClustRes_bestSil_jaspar_homo_sapiens.rds
inst/extdata/motifClustRes_bestSil_jaspar_vert.rds
inst/extdata/motifDistMat_jaspar_Ncor.rds
inst/extdata/motifDistMat_jaspar_homo_sapiens.rds
inst/extdata/motifDistMat_jaspar_mus_musculus.rds
inst/extdata/motifDistMat_jaspar_vert.rds
inst/extdata/tfAnnot_humantfs.rds
man/ChrAccR.Rd
man/DsATAC-class.Rd
man/DsATAC.bam.Rd
man/DsATAC.cellranger.Rd
man/DsATAC.fragmentBed.Rd
man/DsATAC.snakeATAC.Rd
man/DsATACsc-class.Rd
man/DsATACsc.archr.Rd
man/DsATACsc.fragments.Rd
man/DsAcc-class.Rd
man/DsNOMe-class.Rd
man/DsNOMe.bisSNP.Rd
man/PWMatrixToProbMatrix.Rd
man/addSampleAnnotCol-DsAcc-method.Rd
man/aggregateRegionCounts-DsATAC-method.Rd
man/callPeaks-DsATAC-method.Rd
man/cleanMem.Rd
man/colZscores.Rd
man/collapseMotifMatrix.Rd
man/computeDiffAcc.rnb.nome.Rd
man/createReport_differential-DsATAC-method.Rd
man/createReport_exploratory-DsATAC-method.Rd
man/createReport_filtering-DsATAC-method.Rd
man/createReport_normalization-DsATAC-method.Rd
man/createReport_summary-DsATAC-method.Rd
man/dimRed_UMAP-DsATACsc-method.Rd
man/exportCountTracks-DsATAC-method.Rd
man/fastqDirToTable.Rd
man/figures/chraccr_logo.png
man/filterByGRanges-DsATAC-method.Rd
man/filterCellsTssEnrichment-DsATAC-method.Rd
man/filterChroms-DsATAC-method.Rd
man/filterLowCovg-DsATAC-method.Rd
man/findNearestGeneForGr.Rd
man/findOrderedNames.Rd
man/getATACfragments.Rd
man/getChrAccRAnnotationPackage.Rd
man/getChromVarDev-DsATAC-method.Rd
man/getCiceroGeneActivities-DsATAC-method.Rd
man/getComparisonInfo.Rd
man/getComparisonTable-DsAcc-method.Rd
man/getConfigElement.Rd
man/getConsensusPeakSet.Rd
man/getCoord-DsAcc-method.Rd
man/getCounts-DsATAC-method.Rd
man/getCountsSE-DsATAC-method.Rd
man/getCoverage-DsATAC-method.Rd
man/getCovg-DsNOMe-method.Rd
man/getDESeq2Dataset-DsATAC-method.Rd
man/getDiffAcc-DsATAC-method.Rd
man/getFragmentGr-DsATAC-method.Rd
man/getFragmentGrl-DsATAC-method.Rd
man/getFragmentNum-DsATAC-method.Rd
man/getGenome-DsAcc-method.Rd
man/getGenomeObject.Rd
man/getGroupsFromTable.Rd
man/getInsertionKmerFreq-DsATAC-method.Rd
man/getInsertionSites-DsATAC-method.Rd
man/getJasparAnnot.Rd
man/getJasparSymbols.Rd
man/getMeth-DsNOMe-method.Rd
man/getMonocleCellDataSet-DsATAC-method.Rd
man/getMotifClustering.Rd
man/getMotifDistMat.Rd
man/getMotifDistMat.jaspar.Rd
man/getMotifEnrichment-DsATAC-method.Rd
man/getMotifFootprints-DsATAC-method.Rd
man/getMotifOccurrences.Rd
man/getNRegions-DsAcc-method.Rd
man/getNonOverlappingByScore.Rd
man/getPeakSet.snakeATAC.Rd
man/getQuickTssEnrichment-DsATAC-method.Rd
man/getRegionMapping-DsNOMe-method.Rd
man/getRegionTypes-DsAcc-method.Rd
man/getSampleAnnot-DsAcc-method.Rd
man/getSampleMetrics.snakeATAC.Rd
man/getSamples-DsAcc-method.Rd
man/getScQcStatsTab-DsATACsc-method.Rd
man/getTfAnnot.Rd
man/getTssEnrichment-DsATAC-method.Rd
man/getTssEnrichmentBatch-DsATAC-method.Rd
man/hmSeqLogo.Rd
man/isCanonicalChrom.Rd
man/iterativeLSI-DsATACsc-method.Rd
man/join-DsATAC-method.Rd
man/length-DsAcc-method.Rd
man/loadConfig.Rd
man/loadDsAcc.Rd
man/maskMethNA-DsNOMe-method.Rd
man/mergePseudoBulk-DsATACsc-method.Rd
man/mergeSamples-DsATAC-method.Rd
man/mergeStrands-DsNOMe-method.Rd
man/normalizeMeth-DsNOMe-method.Rd
man/plotInsertSizeDistribution-DsATAC-method.Rd
man/prepareMotifmatchr.Rd
man/projectMatrix_UMAP.Rd
man/readMACS2peakFile.Rd
man/regionAggregation-DsATAC-method.Rd
man/regionAggregation-DsNOMe-method.Rd
man/regionSetCounts-DsATAC-method.Rd
man/removeFragmentData-DsATAC-method.Rd
man/removeRegionData-DsATAC-method.Rd
man/removeRegionType-DsATAC-method.Rd
man/removeRegions-DsATAC-method.Rd
man/removeRegions-DsAcc-method.Rd
man/removeRegions-DsNOMe-method.Rd
man/removeSamples-DsATAC-method.Rd
man/rowZscores.Rd
man/run_atac.Rd
man/run_atac_chromvar.Rd
man/run_atac_differential.Rd
man/run_atac_exploratory.Rd
man/run_atac_filtering.Rd
man/run_atac_normalization.Rd
man/run_atac_peakcalling.Rd
man/run_atac_qc.Rd
man/run_atac_sc_unsupervised.Rd
man/safeMatrixStats.Rd
man/samplePseudoBulk-DsATACsc-method.Rd
man/saveConfig.Rd
man/saveDsAcc.Rd
man/setConfigElement.Rd
man/sub-DsATAC-ANY-ANY-ANY-method.Rd
man/transformCounts-DsATAC-method.Rd
man/unsupervisedAnalysisSc-DsATACsc-method.Rd
pkgdown/_pkgdown.yml
pkgdown/extra.css
vignettes/.gitignore
vignettes/articles/images/atac_ia_tb_pca.png
vignettes/articles/images/atac_sc_umap_clusters.png
vignettes/articles/resource.Rmd
vignettes/figures/ChrAccR_overview.png
vignettes/overview.Rmd
vignettes/singlecell.Rmd
