Files in BIMSBbioinfo/RCAS
RNA Centric Annotation System
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/data.R
R/databaseSetUpFunctions.R
R/enrichment_analysis.R
R/meta_analysis_functions.R
R/motif_analysis.R
R/plotting_functions.R
R/report_functions.R
RCAS.Rproj
README.md
data/gff.rda
data/queryRegions.rda
inst/CITATION
inst/NEWS
inst/extdata/EIF4A3Sauliere20121a.bed
inst/extdata/EIF4A3Sauliere20121b.bed
inst/extdata/FMR1_Ascano2012a_hg19.bed
inst/extdata/FMR1_Ascano2012b_hg19.bed
inst/extdata/FUS_Nakaya2013c_hg19.bed
inst/extdata/FUS_Nakaya2013d_hg19.bed
inst/extdata/hg19.RCASDB.sqlite
inst/extdata/hg19.sample.gtf
inst/extdata/hg19.sample.gtf.granges.rds
inst/extdata/msigdb_test.gmt
inst/extdata/testfile.bed
inst/extdata/testfile2.bed
inst/reporting_scripts/footer.html
inst/reporting_scripts/header.html
inst/reporting_scripts/report.Rmd
inst/reporting_scripts/reportMetaAnalysis.Rmd
man/calculateCoverageProfile.Rd
man/calculateCoverageProfileFromTxdb.Rd
man/calculateCoverageProfileList.Rd
man/calculateCoverageProfileListFromTxdb.Rd
man/checkSeqDb.Rd
man/createControlRegions.Rd
man/createDB.Rd
man/createOrthologousGeneSetList.Rd
man/deleteSampleDataFromDB.Rd
man/discoverFeatureSpecificMotifs.Rd
man/extractSequences.Rd
man/findDifferentialMotifs.Rd
man/findEnrichedFunctions.Rd
man/generateKmers.Rd
man/getFeatureBoundaryCoverage.Rd
man/getFeatureBoundaryCoverageBin.Rd
man/getFeatureBoundaryCoverageMulti.Rd
man/getIntervalOverlapMatrix.Rd
man/getMotifSummaryTable.Rd
man/getPWM.Rd
man/getTargetedGenesTable.Rd
man/getTxdbFeatures.Rd
man/getTxdbFeaturesFromGRanges.Rd
man/gff.Rd
man/importBed.Rd
man/importBedFiles.Rd
man/importGtf.Rd
man/parseMsigdb.Rd
man/plotFeatureBoundaryCoverage.Rd
man/printMsigdbDataset.Rd
man/queryGff.Rd
man/queryRegions.Rd
man/retrieveOrthologs.Rd
man/runGSEA.Rd
man/runMotifDiscovery.Rd
man/runMotifRG.Rd
man/runReport.Rd
man/runReportMetaAnalysis.Rd
man/runTopGO.Rd
man/summarizeDatabaseContent.Rd
man/summarizeQueryRegions.Rd
man/summarizeQueryRegionsMulti.Rd
tests/testthat.R
tests/testthat/test_data.R
tests/testthat/test_database_functions.R
tests/testthat/test_motif.R
tests/testthat/test_report.R
tests/testthat/test_txdbfeatures.R
vignettes/RCAS.metaAnalysis.vignette.Rmd
vignettes/RCAS.vignette.Rmd
