Files in JokingHero/ORFik
Open Reading Frames in Genomics

.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/ORFik.R R/ORFs_annotations.R R/ORFs_helpers.R R/RcppExports.R R/cage_annotations.R R/feature_helpers.R R/feature_methods.R R/feature_methods2.R R/find_ORFs.R R/gr_helpers.R R/gr_or_grl_helpers.R R/grl_helpers.R R/ranges_helpers.R R/shift_footprints.R R/shift_footprints_helpers.R R/txdbHelpers.R R/uORF_helpers.R R/utils.R README.md
inst/NEWS
inst/TODO
inst/extdata/annotations.gtf
inst/extdata/cage-seq-heart.bed.bgz
inst/extdata/features.rdata
inst/extdata/genome.fasta
inst/extdata/genome.fasta.fai
inst/extdata/ribo-seq-heart.bed.bgz
inst/extdata/ribo-seq.bam
inst/extdata/ribo-seq.bam.bai
inst/extdata/rna-seq-heart.bed.bgz
man/ORFik-package.Rd man/addCdsOnLeaderEnds.Rd man/addNewTSSOnLeaders.Rd man/asTX.Rd man/assignAnnotations.Rd man/assignFirstExonsStartSite.Rd man/assignLastExonsStopSite.Rd man/assignTSSByCage.Rd man/bedToGR.Rd man/changePointAnalysis.Rd man/checkRFP.Rd man/checkRNA.Rd man/codonSumsPerGroup.Rd man/computeFeatures.Rd man/computeFeaturesCage.Rd man/convertToOneBasedRanges.Rd man/coverageByWindow.Rd man/coveragePerTiling.Rd man/defineIsoform.Rd man/defineTrailer.Rd man/detectRibosomeShifts.Rd man/disengagementScore.Rd man/distToCds.Rd man/distToTSS.Rd man/downstreamFromPerGroup.Rd man/downstreamN.Rd man/downstreamOfPerGroup.Rd man/entropy.Rd man/extendLeaders.Rd man/extendsTSSexons.Rd man/filterCage.Rd man/findCageUTRFivelen.Rd man/findFa.Rd man/findMapORFs.Rd man/findMaxPeaks.Rd man/findNewTSS.Rd man/findORFs.Rd man/findORFsFasta.Rd man/firstEndPerGroup.Rd man/firstExonPerGroup.Rd man/firstStartPerGroup.Rd man/floss.Rd man/fpkm.Rd man/fpkm_calc.Rd man/fractionLength.Rd man/fread.bed.Rd man/gSort.Rd man/getStartStopWindows.Rd man/groupGRangesBy.Rd man/hasHits.Rd man/initiationScore.Rd man/insideOutsideORF.Rd man/is.gr_or_grl.Rd man/is.grl.Rd man/isInFrame.Rd man/isOverlapping.Rd man/isPeriodic.Rd man/kozakSequenceScore.Rd man/lastExonEndPerGroup.Rd man/lastExonPerGroup.Rd man/lastExonStartPerGroup.Rd man/longestORFs.Rd man/makeExonRanks.Rd man/makeORFNames.Rd man/mapToGRanges.Rd man/matchNaming.Rd man/metaWindow.Rd man/numExonsPerGroup.Rd man/orfID.Rd man/orfScore.Rd man/overlapsToCoverage.Rd man/parseCigar.Rd man/rankOrder.Rd man/readWidths.Rd man/reassignTSSbyCage.Rd man/reassignTxDbByCage.Rd man/reduceKeepAttr.Rd man/regroupRleList.Rd man/remakeTxdbExonIds.Rd man/removeMetaCols.Rd man/removeTxdbExons.Rd man/restrictTSSByUpstreamLeader.Rd man/riboTISCoverageProportion.Rd man/ribosomeReleaseScore.Rd man/ribosomeStallingScore.Rd man/seqnamesPerGroup.Rd man/shiftFootprints.Rd man/sortPerGroup.Rd man/startCodons.Rd man/startDefinition.Rd man/startRegionString.Rd man/startSites.Rd man/stopCodons.Rd man/stopDefinition.Rd man/stopSites.Rd man/strandBool.Rd man/strandPerGroup.Rd man/subsetCoverage.Rd man/subset_to_frame.Rd man/tile1.Rd man/translationalEff.Rd man/txLen.Rd man/txNames.Rd man/txNamesWithLeaders.Rd man/txSeqsFromFa.Rd man/uORFSearchSpace.Rd man/uniqueGroups.Rd man/uniqueOrder.Rd man/unlistGrl.Rd man/updateTxdbRanks.Rd man/updateTxdbStartSites.Rd man/upstreamOfPerGroup.Rd man/validExtension.Rd man/validGRL.Rd man/widthPerGroup.Rd man/windowPerGroup.Rd
src/.gitignore
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/findORFsHelpers.cpp
src/findORFsHelpers.h
src/findOrfs.cpp
src/findOrfsFasta.cpp
tests/testthat.R tests/testthat/test_ORFs_helpers.R tests/testthat/test_cage.R tests/testthat/test_cds_helpers.R tests/testthat/test_features.R tests/testthat/test_granges_helpers.R tests/testthat/test_shift_footprints.R vignettes/ORFikOverview.Rmd
JokingHero/ORFik documentation built on Sept. 20, 2018, 1:26 p.m.