Files in mireia-bioinfo/pipelineNGS
Methods for Epigenetic Data Processing
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/alignmentBowtie2.R
R/bamToVis.R
R/callPeak.R
R/fastqc.R
R/filtOutBAM.R
R/getNameFromPath.R
R/getStats.R
R/mergeBAMs.R
R/offsetATAC.R
R/paramdata.R
R/pipelineNGS.R
R/plotStats.R
R/process.R
R/processCUTTAG.R
R/sysdata.rda
R/trim_adapters.R
README.md
_pkgdown.yml
data/paramdata.rda
docs/404.html
docs/articles/CUT&TAG_processing_pipeline.html
docs/articles/figures/process_epi_map.png
docs/articles/index.html
docs/articles/introduction.html
docs/articles/introduction_files/figure-html/unnamed-chunk-5-1.png
docs/articles/introduction_files/figure-html/unnamed-chunk-6-1.png
docs/authors.html
docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js
docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.1.0/bootstrap.min.css
docs/deps/data-deps.txt
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/alignmentBowtie2.html
docs/reference/bamToBigWig.html
docs/reference/callPeak.html
docs/reference/dot-getBDGforSEACR.html
docs/reference/fastqc.html
docs/reference/filtOutBAM.html
docs/reference/getNameFromPath.html
docs/reference/getStats.html
docs/reference/index.html
docs/reference/mergeBAMs.html
docs/reference/offsetATAC.html
docs/reference/offsetATACSE.html
docs/reference/paramdata.html
docs/reference/peakCallingSEACR.html
docs/reference/pipelineNGS.html
docs/reference/plotAlignment.html
docs/reference/processCUTTAG.html
docs/reference/process_epigenome.html
docs/reference/tableFromIdxstats.html
inst/extdata/Logs/HI19.alignment.log
inst/extdata/Logs/HI19.idxstats.log
inst/extdata/Logs/HI19.macs2.log
inst/extdata/Logs/HI19.raw.idxstats.log
inst/extdata/Logs/HI19.rmdup.log
inst/extdata/Logs/HI22.alignment.log
inst/extdata/Logs/HI22.idxstats.log
inst/extdata/Logs/HI22.macs2.log
inst/extdata/Logs/HI22.raw.idxstats.log
inst/extdata/Logs/HI22.rmdup.log
inst/extdata/Logs/HI37.alignment.log
inst/extdata/Logs/HI37.idxstats.log
inst/extdata/Logs/HI37.macs2.log
inst/extdata/Logs/HI37.raw.idxstats.log
inst/extdata/Logs/HI37.rmdup.log
inst/extdata/Logs/HI40.alignment.log
inst/extdata/Logs/HI40.idxstats.log
inst/extdata/Logs/HI40.macs2.log
inst/extdata/Logs/HI40.raw.idxstats.log
inst/extdata/Logs/HI40.rmdup.log
inst/extdata/Peaks/HI19_peaks.broadPeak
inst/extdata/Peaks/HI22_peaks.broadPeak
inst/extdata/Peaks/HI37_peaks.broadPeak
inst/extdata/Peaks/HI40_peaks.broadPeak
inst/extdata/parameters.csv
inst/scripts/download_placentalmammals_cons.R
man/alignmentBowtie2.Rd
man/bamToBigWig.Rd
man/callPeak.Rd
man/dot-getBDGforSEACR.Rd
man/fastqc.Rd
man/filtOutBAM.Rd
man/getNameFromPath.Rd
man/getStats.Rd
man/mergeBAMs.Rd
man/offsetATAC.Rd
man/offsetATACSE.Rd
man/paramdata.Rd
man/peakCallingSEACR.Rd
man/pipelineNGS.Rd
man/plotAlignment.Rd
man/processCUTTAG.Rd
man/process_epigenome.Rd
man/tableFromIdxstats.Rd
pipelineNGS.Rproj
vignettes/figures/align_postpro.png
vignettes/figures/align_postpro.svg
vignettes/figures/align_postproc.png
vignettes/figures/process_epi_map.png
vignettes/introduction.Rmd
