Files in ssayols/dupRadar
Assessment of duplication rates in RNA-Seq datasets
.BBSoptions
.Rbuildignore
.github/.gitignore
.github/workflows/pkgdown.yaml
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/analyzeDuprates.R
R/cumulativeDuprateBarplot.R
R/dupRadar-package.R
R/duprateExpBoxplot.R
R/duprateExpDensPlot.R
R/duprateExpFit.R
R/duprateExpIdentify.R
R/duprateExpPlot.R
R/expressionHist.R
R/getBinDuplication.R
R/getBinRpkMean.R
R/getDupMatBin.R
R/getDupMatStats.R
R/getDynamicRange.R
R/getRpkBinReadCountFraction.R
R/getRpkCumulativeReadCountFraction.R
R/markDuplicates.R
R/readcountExpBoxplot.R
README.md
_pkgdown.yml
data/datalist
data/dupRadar_examples.RData
docs/404.html
docs/LICENSE-text.html
docs/articles/dupRadar.html
docs/articles/dupRadar_files/anchor-sections-1.0/anchor-sections.css
docs/articles/dupRadar_files/anchor-sections-1.0/anchor-sections.js
docs/articles/dupRadar_files/figure-html/unnamed-chunk-10-1.png
docs/articles/dupRadar_files/figure-html/unnamed-chunk-12-1.png
docs/articles/dupRadar_files/figure-html/unnamed-chunk-13-1.png
docs/articles/dupRadar_files/figure-html/unnamed-chunk-5-1.png
docs/articles/dupRadar_files/figure-html/unnamed-chunk-5-2.png
docs/articles/dupRadar_files/figure-html/unnamed-chunk-6-1.png
docs/articles/dupRadar_files/figure-html/unnamed-chunk-8-1.png
docs/articles/dupRadar_files/figure-html/unnamed-chunk-9-1.png
docs/articles/figures/GCcontent.svg
docs/articles/figures/GCdependence.png
docs/articles/figures/encode.svg
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/analyzeDuprates.html
docs/reference/bamutilMarkDuplicates.html
docs/reference/cumulativeDuprateBarplot-1.png
docs/reference/cumulativeDuprateBarplot.html
docs/reference/dm.bad.html
docs/reference/dm.html
docs/reference/dupRadar.html
docs/reference/dupRadar_examples.html
docs/reference/duprateExpBoxplot-1.png
docs/reference/duprateExpBoxplot.html
docs/reference/duprateExpDensPlot-1.png
docs/reference/duprateExpDensPlot.html
docs/reference/duprateExpFit.html
docs/reference/duprateExpIdentify-1.png
docs/reference/duprateExpIdentify.html
docs/reference/duprateExpPlot-1.png
docs/reference/duprateExpPlot.html
docs/reference/expressionHist-1.png
docs/reference/expressionHist.html
docs/reference/getBinDuplication.html
docs/reference/getBinRpkMean.html
docs/reference/getDupMatBin.html
docs/reference/getDupMatStats.html
docs/reference/getDynamicRange.html
docs/reference/getRpkBinReadCountFraction.html
docs/reference/getRpkCumulativeReadCountFraction.html
docs/reference/index.html
docs/reference/markDuplicates.html
docs/reference/picardMarkDuplicates.html
docs/reference/readcountExpBoxplot-1.png
docs/reference/readcountExpBoxplot.html
docs/sitemap.xml
inst/CITATION
inst/extdata/genes.gtf
inst/extdata/wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam
inst/extdata/wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam.bai
inst/extdata/wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2_duprm.bam
inst/extdata/wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2_duprm.bam.log
man/analyzeDuprates.Rd
man/bamutilMarkDuplicates.Rd
man/cumulativeDuprateBarplot.Rd
man/dm.Rd
man/dm.bad.Rd
man/dupRadar.Rd
man/dupRadar_examples.Rd
man/duprateExpBoxplot.Rd
man/duprateExpDensPlot.Rd
man/duprateExpFit.Rd
man/duprateExpIdentify.Rd
man/duprateExpPlot.Rd
man/expressionHist.Rd
man/getBinDuplication.Rd
man/getBinRpkMean.Rd
man/getDupMatBin.Rd
man/getDupMatStats.Rd
man/getDynamicRange.Rd
man/getRpkBinReadCountFraction.Rd
man/getRpkCumulativeReadCountFraction.Rd
man/markDuplicates.Rd
man/picardMarkDuplicates.Rd
man/readcountExpBoxplot.Rd
vignettes/dupRadar.Rmd
vignettes/figures/GCcontent.svg
vignettes/figures/GCdependence.png
vignettes/figures/encode.svg
