Files in sheffien/LOLA
Locus overlap analysis for enrichment of genomic ranges
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R/LOLA.R
R/calcLocEnrichment.R
R/data.R
R/examples/example.R
R/examples/example2.R
R/loadRegionDB.R
R/postEnrichment.R
R/splitFileIntoCollection.R
R/utility.R
README.md
_pkgdown.yaml
data/sample_input.RData
data/sample_universe.RData
inst/CITATION
inst/extdata/examples/combined_regions.bed
inst/extdata/hg19/ucsc_example/collection.txt
inst/extdata/hg19/ucsc_example/index.txt
inst/extdata/hg19/ucsc_example/regions/cpgIslandExt.bed
inst/extdata/hg19/ucsc_example/regions/laminB1Lads.bed
inst/extdata/hg19/ucsc_example/regions/numtSAssembled.bed
inst/extdata/hg19/ucsc_example/regions/vistaEnhancers.bed
inst/extdata/hg19/ucsc_example/regions/vistaEnhancers_colNames.bed
inst/extdata/hg19/ucsc_example/sizes.txt
inst/extdata/multi/collection1/collection.txt
inst/extdata/multi/collection1/index.txt
inst/extdata/multi/collection1/regions/cpgIslandExt.bed
inst/extdata/multi/collection1/regions/laminB1Lads.bed
inst/extdata/multi/collection1/regions/vistaEnhancers.bed
inst/extdata/multi/collection1/sizes.txt
inst/extdata/multi/collection2/index.txt
inst/extdata/multi/collection2/regions/cpgIslandExt.bed
inst/extdata/multi/collection2/regions/laminB1Lads.bed
inst/extdata/multi/collection2/regions/vistaEnhancers.bed
inst/extdata/multi/collection2/sizes.txt
inst/scripts/LOLA
inst/web/README.md
inst/web/allEnrichments.tsv
inst/web/index.html
inst/web/webComponents/ajax-loader.gif
inst/web/webComponents/d3.min.js
inst/web/webComponents/gridstyle.css
man/LOLA.Rd
man/buildRestrictedUniverse.Rd
man/checkUniverseAppropriateness.Rd
man/cleanws.Rd
man/countOverlapsAnyRev.Rd
man/extractEnrichmentOverlaps.Rd
man/figures/LOLA-logo.png
man/getRegionFile.Rd
man/getRegionSet.Rd
man/lapplyAlias.Rd
man/listRegionSets.Rd
man/listToGRangesList.Rd
man/loadRegionDB.Rd
man/mergeRegionDBs.Rd
man/nlist.Rd
man/plotTopLOLAEnrichments.Rd
man/readBed.Rd
man/readCollection.Rd
man/readCollectionAnnotation.Rd
man/readCollectionFiles.Rd
man/readRegionGRL.Rd
man/readRegionSetAnnotation.Rd
man/redefineUserSets.Rd
man/replaceFileExtension.Rd
man/runLOLA.Rd
man/sampleGRL.Rd
man/setLapplyAlias.Rd
man/setSharedDataDir.Rd
man/splitDataTable.Rd
man/splitFileIntoCollection.Rd
man/userSets.Rd
man/userUniverse.Rd
man/write.tsv.Rd
man/writeCombinedEnrichment.Rd
man/writeDataTableSplitByColumn.Rd
tests/testthat.R
tests/testthat/test_all.R
vignettes/choosingUniverse.Rmd
vignettes/gettingStarted.Rmd
vignettes/usingLOLACore.Rmd
