Files in betsig/GeneStructureTools
Tools for spliced gene structure manipulation and analysis
.Rbuildignore
.gitignore
DESCRIPTION
GeneStructureTools.Rproj
LICENSE
NAMESPACE
R/AltSplicingJunctionSupported.R
R/ExonSkipping.R
R/IntronRetention.R
R/UTR2UTR53.R
R/altSplicingrMATS.R
R/altTransStartEnd.R
R/classes.R
R/compareTranscripts.R
R/exonReformatting.R
R/helpers.R
R/leafCutter.R
R/longestORF.R
R/plotGvisTracks.R
R/quickAnalysis.R
R/quickIrfinder.R
R/quickRmats.R
R/quickWhippet.R
R/readWhippetFiles.R
README.md
inst/NEWS
inst/extdata/gencode.vM25.small.gtf
inst/extdata/irf_small/00_v_48.txt
inst/extdata/leaf_small/A_000.junc
inst/extdata/leaf_small/A_048.junc
inst/extdata/leaf_small/B_000.junc
inst/extdata/leaf_small/B_048.junc
inst/extdata/leaf_small/per_intron_results.tab
inst/extdata/leafcutter2table.R
inst/extdata/leafviz2table.R
inst/extdata/prepare_results.R
inst/extdata/rmats_small/A3SS.MATS.JC.txt
inst/extdata/rmats_small/A5SS.MATS.JC.txt
inst/extdata/rmats_small/MXE.MATS.JC.txt
inst/extdata/rmats_small/RI.MATS.JC.txt
inst/extdata/rmats_small/SE.MATS.JC.txt
inst/extdata/whippet_small/00_v_48.diff.gz
inst/extdata/whippet_small/A_000_whippet.jnc.gz
inst/extdata/whippet_small/A_000_whippet.psi.gz
inst/extdata/whippet_small/A_048_whippet.jnc.gz
inst/extdata/whippet_small/A_048_whippet.psi.gz
inst/extdata/whippet_small/B_000_whippet.jnc.gz
inst/extdata/whippet_small/B_000_whippet.psi.gz
inst/extdata/whippet_small/B_048_whippet.jnc.gz
inst/extdata/whippet_small/B_048_whippet.psi.gz
man/UTR2UTR53.Rd
man/addIntronInTranscript.Rd
man/addSets.Rd
man/altIntronRmats.Rd
man/altSpliceSiteRmats.Rd
man/alterTranscriptStartEnds.Rd
man/alternativeIntronUsage.Rd
man/annotateEventCoords.Rd
man/annotateGeneModel.Rd
man/annotateOverlapRmats.Rd
man/attrChangeAltSpliced.Rd
man/betweenNumbers.Rd
man/compareContains.Rd
man/coordinates-methods.Rd
man/cumsumANDpad.Rd
man/diffSplicingResults-methods.Rd
man/duplicateReference.Rd
man/exonsToIntrons.Rd
man/exonsToTranscripts.Rd
man/extractEvent-methods.Rd
man/featureTypes.Rd
man/filterIrfEvents.Rd
man/filterRmatsEvents.Rd
man/filterWhippetEvents.Rd
man/findExonContainingTranscripts.Rd
man/findIntronContainingTranscripts.Rd
man/findJunctionPairs.Rd
man/findOverlaps.junc.Rd
man/formatWhippetEvents.Rd
man/getOrfs.Rd
man/getUOrfs.Rd
man/irfDataSet-class.Rd
man/irfResults-methods.Rd
man/irfTranscriptChangeSummary.Rd
man/junctions-methods.Rd
man/leafcutterIntronsToExons.Rd
man/leafcutterTranscriptChangeSummary.Rd
man/makeGeneModel.Rd
man/makeNewLeafExons.Rd
man/makeNewLeafExonsUnanchored.Rd
man/matrix2combinations.Rd
man/maxLocation.Rd
man/orfDiff.Rd
man/orfSimilarity.Rd
man/overlap2matrix.Rd
man/readCounts-methods.Rd
man/readIrfDataSet.Rd
man/readLeafcutterJunctions.Rd
man/readRmatsDataSet.Rd
man/readWhippetDIFFfiles.Rd
man/readWhippetDataSet.Rd
man/readWhippetJNCfiles.Rd
man/readWhippetPSIfiles.Rd
man/reformatExons.Rd
man/removeDuplicatePairs.Rd
man/removeDuplicateTranscripts.Rd
man/removeExonsBetween.Rd
man/removeSameExon.Rd
man/removeVersion.Rd
man/reorderExonNumbers.Rd
man/replaceJunction.Rd
man/rmatsDataSet-class.Rd
man/rmatsTranscriptChangeSummary.Rd
man/skipExonByJunction.Rd
man/skipExonInTranscript.Rd
man/splitLongExons.Rd
man/transcriptChangeSummary.Rd
man/whippetDataSet-class.Rd
man/whippetTranscriptChangeSummary.Rd
vignettes/Eif4a2_clu_1396.png
vignettes/HexLogoGeneStructureTools.png
vignettes/Pdlim7_clu_4466.png
vignettes/Rnps1_clu_1281.png
vignettes/Supt5_clu_21794.png
vignettes/Vignette.Rmd
vignettes/transcript_types_broad_table
vignettes/transcript_types_broad_table.txt
vignettes/whippetAltAceDon.png
vignettes/whippetAltFirstLast.png
vignettes/whippetExonSkip.png
vignettes/whippetIntronRetention.png
