Files in GreenleafLab/ChrAccR
Analyzing chromatin accessibility data in R

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/ChrAccR.R R/DsATAC-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/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
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.fragmentBed.Rd man/DsATAC.snakeATAC.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/exportCountTracks-DsATAC-method.Rd man/fastqDirToTable.Rd
man/figures/chraccr_logo.png
man/filterByGRanges-DsATAC-method.Rd man/filterChroms-DsATAC-method.Rd man/filterLowCovg-DsATAC-method.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/getTfAnnot.Rd man/getTssEnrichment-DsATAC-method.Rd man/getTssEnrichmentBatch-DsATAC-method.Rd man/hmSeqLogo.Rd man/isCanonicalChrom.Rd man/length-DsAcc-method.Rd man/loadConfig.Rd man/loadDsAcc.Rd man/maskMethNA-DsNOMe-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/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_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/saveConfig.Rd man/saveDsAcc.Rd man/setConfigElement.Rd man/sub-DsATAC-ANY-ANY-ANY-method.Rd man/transformCounts-DsATAC-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
GreenleafLab/ChrAccR documentation built on April 28, 2020, 1:55 a.m.