Files in Roleren/uORFomePipe
uORF prediction in R
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/.Rhistory
R/Classifier.R
R/ClassifierHelpers.R
R/ClassifierStats.R
R/ClassifierTrainingData.R
R/DataBaseCreator.R
R/DataBaseGetters.R
R/DataBaseGroupers.R
R/DataBaseValidation.R
R/GO_analysis.R
R/GRangesHelpers.R
R/GenomicGetters.R
R/Init.R
R/PipelineParts.R
R/TissueTables.R
R/Utils.R
R/databaseHelpers.R
R/features.R
README.md
inst/extdata/analysis_plot.png
inst/extdata/atf4a_uORF.png
man/allLeadersSpanningLeader.Rd
man/artificial.from.cds.Rd
man/atlasTissue.Rd
man/checkAndInitPipe.Rd
man/createCatalogueDB.Rd
man/createDataBase.Rd
man/createGRObjects.Rd
man/createUORFAtlas.Rd
man/createUniqueIDs.Rd
man/deleteDataBase.Rd
man/deleteTable.Rd
man/deleteUorfTables.Rd
man/feature.boxplots.Rd
man/featureAnalysis.Rd
man/findClassificationBoundary.Rd
man/find_uORFome.Rd
man/fixNAandINFTable.Rd
man/forest.Rd
man/getAll.Rd
man/getAllLeaderChanges.Rd
man/getAllORFGeneSymbols.Rd
man/getAllSequenceFeaturesTable.Rd
man/getAllUORFData.Rd
man/getBestIsoformStartCodonCoverage.Rd
man/getBiomartFromOrganism.Rd
man/getCDS.Rd
man/getCDSFiltered.Rd
man/getCDSTraining.Rd
man/getCageTx.Rd
man/getCandidateuORFs.Rd
man/getFasta.Rd
man/getGTF.Rd
man/getGeneralRiboFeatures.Rd
man/getIDsFromUorfs.Rd
man/getLeaders.Rd
man/getLeadersFromCage.Rd
man/getORFNamesDB.Rd
man/getORFsGoTerms.Rd
man/getSequenceFeatures.Rd
man/getSpecialThreeUTRs.Rd
man/getThreeUTRs.Rd
man/getTissueFromFeatureTable.Rd
man/getTissueTable.Rd
man/getTx.Rd
man/getUorfsInDb.Rd
man/insertTable.Rd
man/leaderCage.Rd
man/linkORFsToTx.Rd
man/listTables.Rd
man/makeCombinedPrediction.Rd
man/makeORFPredictionData.Rd
man/makeTrainingAndPredictionData.Rd
man/makeTrainingData.Rd
man/matchByTranscript.Rd
man/p.Rd
man/pcaCAGEValidation.Rd
man/perSampleCountPlot.Rd
man/predictUorfs.Rd
man/predictionVsCageHits.Rd
man/readTable.Rd
man/removeIDColumns.Rd
man/sequenceClassifier.Rd
man/startAndStopCodonPlots.Rd
man/startCodonMetrics.Rd
man/strongCDS.Rd
man/subset.ORF.Rd
man/tableNotExists.Rd
man/test.artificial.Rd
man/toGRFromUniqueID.Rd
man/trainClassifier.Rd
man/validateExperiments.Rd
man/validateInputs.Rd
man/validateStartCodons.Rd
man/varianceTissueUsage.Rd
man/venn.diagram.uORFs.Rd
man/verification.conf.matrix.Rd
man/weakTrailer.Rd
uORFomePipe.Rproj
