Files in biobenkj/ATACseeker
Utilities for ATACseq QC, differential accessibility, and integration
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/atacPairedEnd.R
R/collectStats.R
R/estK.R
R/fragPlot.R
R/fragmentLengths.R
R/get5primeCuts.R
R/getComplexity.R
R/getEnds.R
R/getEsts.R
R/getFeatureCounts.R
R/getQC.R
R/plotComplexity.R
R/plotCoverage.R
R/plotStranded.R
R/processUcscCytoband.R
R/ruvNorm.R
R/shrinkPairs.R
R/tssQcPlot.R
README.md
data/CTCFsites.hg19.rda
data/CTCFsites.mm10.rda
data/cytobands_hg19.rda
data/cytobands_hg38.rda
data/cytobands_mm10.rda
data/cytobands_mm9.rda
inst/extdata/blacklists/BLACKLIST_CITATION
inst/extdata/blacklists/hg19.blacklist.ENCFF001TDO.bed.gz
inst/extdata/blacklists/hg38.blacklist.ENCFF419RSJ.bed.gz
inst/extdata/blacklists/mm10.blacklist.bed.gz
inst/extdata/blacklists/mm9-blacklist.bed.gz
inst/extdata/bulkATACexampleBAMs/bulkAtacCovariates.csv
inst/extdata/csawExampleData/csaw_global_filtered.RData
inst/extdata/dnasePeaks/REMC_blood_regions_merged.hg19.bed.gz
inst/extdata/liftOver/hg19ToHg38.over.chain
inst/extdata/liftOver/hg19TorCRS.chain
inst/extdata/scATACexampleBAMs/combined_scATAC_runs.csv
inst/extdata/scATACexampleBAMs/phenotype_info.txt
inst/extdata/tss/hg19_gencode_tss_unique.bed.gz
inst/extdata/tss/hg38_gencode_tss_unique.bed.gz
inst/extdata/tss/mm10_gencode_tss_unique.bed.gz
inst/extdata/tss/mm9_gencode_tss_unique.bed.gz
man/ATACseeker-package.Rd
man/atacPairedEnd.Rd
man/collectStats.Rd
man/estK.Rd
man/fragPlot.Rd
man/fragmentLengths.Rd
man/get5primeCuts.Rd
man/getComplexity.Rd
man/getEnds.Rd
man/getEsts.Rd
man/getFeatureCounts.Rd
man/getQC.Rd
man/plotComplexity.Rd
man/plotCoverage.Rd
man/plotStranded.Rd
man/processUcscCytoband.Rd
man/ruvNorm.Rd
man/shrinkPairs.Rd
man/tssQcPlot.Rd
tests/test-all.R
tests/testthat/test.R
vignettes/ATACseeker_vignette.Rmd
