Files in Mathelab/ALTRE
Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data
.Rbuildignore
.gitattributes
.gitignore
.travis.yml
ALTRE.Rproj
DESCRIPTION
NAMESPACE
R/1_getfiles.R
R/2_getconsensus.R
R/3_getannotation.R
R/4_getcountsWindows.R
R/4_getcountsfast.R
R/5_getaltered.R
R/6_getcategorized.R
R/7_getcomparison.R
R/8_runGREATpathway.R
R/8b_runChipEnrich.R
R/ALTRE.R
R/internalfunctions.R
R/plottingfunctions.R
R/runshiny.R
R/writerfunctions.R
README.md
appveyor.yml
inst/NEWS
inst/img/ALTREinstall.gif
inst/img/ALTREprev.gif
inst/img/ALTRErun.gif
inst/shinyApp/global.R
inst/shinyApp/include.md
inst/shinyApp/server.R
inst/shinyApp/ui.R
inst/shinyApp/www/custom.css
man/ALTRE.Rd
man/categAltrePeaks.Rd
man/combineAnnotatePeaks.Rd
man/comparePeaksAltre.Rd
man/countanalysis.Rd
man/getConsensusPeaks.Rd
man/getCounts.Rd
man/getCountsFast.Rd
man/getTSS.Rd
man/grangestodataframe.Rd
man/loadBamFiles.Rd
man/loadBedFiles.Rd
man/loadCSVFile.Rd
man/mergeclosepeaks.Rd
man/plotCombineAnnotatePeaks.Rd
man/plotCompareMethods.Rd
man/plotCompareMethodsAll.Rd
man/plotConsensusPeaks.Rd
man/plotCountAnalysis.Rd
man/plotDistCountAnalysis.Rd
man/plotGREATenrich.Rd
man/plotGetCounts.Rd
man/processPathways.Rd
man/runGREAT.Rd
man/runShinyApp.Rd
man/statscombineannotate.Rd
man/tssannotgrange.Rd
man/writeBedFile.Rd
man/writeCompareRE.Rd
man/writeConsensusRE.Rd
man/writeGREATpath.Rd
