Files in LOLA

Locus overlap analysis for enrichment of genomic ranges

README.md

NEWS

NAMESPACE

DESCRIPTION

build/vignette.rds

data/sample_input.RData

data/sample_universe.RData

R/calcLocEnrichment.R R/splitFileIntoCollection.R R/utility.R R/LOLA.R R/loadRegionDB.R R/postEnrichment.R R/data.R R/examples/example.R R/examples/example2.R vignettes/choosingUniverse.Rmd vignettes/gettingStarted.Rmd vignettes/usingLOLACore.Rmd man/write.tsv.Rd man/LOLA.Rd man/plotTopLOLAEnrichments.Rd man/splitDataTable.Rd man/countOverlapsAnyRev.Rd man/readCollectionFiles.Rd man/userUniverse.Rd man/buildRestrictedUniverse.Rd man/splitFileIntoCollection.Rd man/nlist.Rd man/readCollection.Rd man/getRegionFile.Rd man/extractEnrichmentOverlaps.Rd man/readCollectionAnnotation.Rd man/sampleGRL.Rd man/mergeRegionDBs.Rd man/setSharedDataDir.Rd man/cleanws.Rd man/loadRegionDB.Rd man/userSets.Rd man/listToGRangesList.Rd man/getRegionSet.Rd man/replaceFileExtension.Rd man/checkUniverseAppropriateness.Rd man/writeCombinedEnrichment.Rd man/runLOLA.Rd man/redefineUserSets.Rd man/readRegionGRL.Rd man/readBed.Rd man/listRegionSets.Rd man/lapplyAlias.Rd man/setLapplyAlias.Rd man/writeDataTableSplitByColumn.Rd man/readRegionSetAnnotation.Rd

man/figures/LOLA-logo.png

tests/testthat.R tests/testthat/test_all.R

inst/CITATION

inst/doc/usingLOLACore.html

inst/doc/gettingStarted.R inst/doc/choosingUniverse.R inst/doc/usingLOLACore.R

inst/doc/gettingStarted.html

inst/doc/choosingUniverse.Rmd inst/doc/gettingStarted.Rmd

inst/doc/choosingUniverse.html

inst/doc/usingLOLACore.Rmd

inst/web/index.html

inst/web/allEnrichments.tsv

inst/web/README.md

inst/web/webComponents/gridstyle.css

inst/web/webComponents/ajax-loader.gif

inst/web/webComponents/d3.min.js

inst/extdata/hg19/ucsc_example/sizes.txt

inst/extdata/hg19/ucsc_example/index.txt

inst/extdata/hg19/ucsc_example/collection.txt

inst/extdata/hg19/ucsc_example/regions/vistaEnhancers.bed

inst/extdata/hg19/ucsc_example/regions/numtSAssembled.bed

inst/extdata/hg19/ucsc_example/regions/vistaEnhancers_colNames.bed

inst/extdata/hg19/ucsc_example/regions/laminB1Lads.bed

inst/extdata/hg19/ucsc_example/regions/cpgIslandExt.bed

inst/extdata/examples/combined_regions.bed

inst/extdata/multi/collection2/sizes.txt

inst/extdata/multi/collection2/index.txt

inst/extdata/multi/collection2/regions/vistaEnhancers.bed

inst/extdata/multi/collection2/regions/laminB1Lads.bed

inst/extdata/multi/collection2/regions/cpgIslandExt.bed

inst/extdata/multi/collection1/sizes.txt

inst/extdata/multi/collection1/index.txt

inst/extdata/multi/collection1/collection.txt

inst/extdata/multi/collection1/regions/vistaEnhancers.bed

inst/extdata/multi/collection1/regions/laminB1Lads.bed

inst/extdata/multi/collection1/regions/cpgIslandExt.bed

inst/scripts/LOLA

LOLA documentation built on Nov. 8, 2020, 8:23 p.m.