Files in RamsinghLab/ATACseeker
Utilities for ATACseq QC, differential accessibility, and integration

.gitignore
DESCRIPTION
NAMESPACE
R/addMtGeneLabel.R R/atacPairedEnd.R R/callMT.R R/collectStats.R R/fragPlot.R R/fragmentLengths.R R/get5primeCuts.R R/getComplexity.R R/getEnds.R R/getEsts.R R/getFeatureCounts.R R/getMT.R R/getQC.R R/plotComplexity.R R/plotCoverage.R R/plotMT.R R/plotStranded.R R/processUcscCytoband.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
data/mtGenes.hg19.rda
data/mtGenes.hg38.rda
data/txsByFpkmInMouseLskCells.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/liftOver/hg19ToHg38.over.chain
inst/extdata/makeMtGeneGRanges.R
inst/extdata/mitomes/GRCh37.MT.fasta
inst/extdata/mitomes/GRCh38.MT.fasta
inst/extdata/mitomes/hg19.chrM.fasta
inst/extdata/mitomes/hg38.chrM.fasta
inst/extdata/mitomes/mm10.chrM.fasta
inst/extdata/mitomes/mm9.chrM.fasta
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/addMtGeneLabel.Rd man/atacPairedEnd.Rd man/callMT.Rd man/collectStats.Rd man/fragPlot.Rd man/fragmentLengths.Rd man/get5primeCuts.Rd man/getComplexity.Rd man/getEnds.Rd man/getEsts.Rd man/getFeatureCounts.Rd man/getMT.Rd man/getQC.Rd man/plotComplexity.Rd man/plotCoverage.Rd man/plotMT.Rd man/plotStranded.Rd man/processUcscCytoband.Rd man/shrinkPairs.Rd man/tssQcPlot.Rd vignette/WRITE_ME.Rmd
RamsinghLab/ATACseeker documentation built on April 15, 2018, 4:19 p.m.