Man pages for Roleren/uORFomePipe
uORF prediction in R
| allLeadersSpanningLeader | Make a leader that spans the max leader per transcript by... |
| artificial.from.cds | Artificial ORFs from CDS |
| atlasTissue | Group feature table by tissue 1st table is filtered on fpkm >... |
| checkAndInitPipe | Init uORFome pipeline |
| createCatalogueDB | Main function to fill uORF database |
| createDataBase | Create the database for uORFome |
| createGRObjects | convert to gr from string and filter NB!!! put this in... |
| createUniqueIDs | Create 1 column of all unique ids from uorfID folder |
| createUORFAtlas | Create cage ATLAS of uORFs, per CAGE sample, does uORF exist... |
| deleteDataBase | Delete the database for uORFome |
| deleteTable | Delete single sql table |
| deleteUorfTables | Delete uorf tables |
| featureAnalysis | General feature analysis |
| feature.boxplots | Box plot of feature difference between active and inactive... |
| findClassificationBoundary | Classification bounaries |
| find_uORFome | Run whole uORFomePipe prediction |
| fixNAandINFTable | Remove infinite and NAs in matrix |
| forest | Train h2o rf model. negDT if you want own samples for that |
| getAll | Get all annotation parts leader, cds, threeUTRs and tx |
| getAllLeaderChanges | Get variance between different leader versions |
| getAllORFGeneSymbols | Get gene symbols from ensemble gene names |
| getAllSequenceFeaturesTable | Get all sequence features for ORFs |
| getAllUORFData | Get all data for combined dataset |
| getBestIsoformStartCodonCoverage | A filter per stop codon group |
| getBiomartFromOrganism | Guess biomart from organism name |
| getCageTx | New leaders defined as maximum upstream for each original... |
| getCandidateuORFs | Find uORFs from new leader regions |
| getCDS | Get the coding sequences from the gtf file |
| getCDSFiltered | Get CDS that were filtered |
| getCDSTraining | Get CDS used for positive training set |
| getFasta | Get the fasta indexed file |
| getGeneralRiboFeatures | Get Ribo-seq features |
| getGTF | Get the Genomic transcript format, currently using GRch38... |
| getIDsFromUorfs | Find unique uORF ID's from uORFs |
| getLeaders | Get the 5' leaders |
| getLeadersFromCage | Reassign leaders by CAGE |
| getORFNamesDB | Get orf names from the orf data-base |
| getORFsGoTerms | Get Go terms |
| getSequenceFeatures | Get sequence features from orfik |
| getSpecialThreeUTRs | Used as negative set for training |
| getThreeUTRs | Get the 3' sequences from the gtf file |
| getTissueFromFeatureTable | Get specific feature for specific tissues |
| getTissueTable | Create tissueTable for cage, 1 row per unique uorf Tissue... |
| getTx | Get transcripts from gtf |
| getUorfsInDb | get the uorfs in the database |
| insertTable | Delete the database for uORFome |
| leaderCage | Get maximum spanning CAGE leaders |
| linkORFsToTx | Assign transcriptnames to orfs, and find rank for each orf |
| listTables | List current tables in database |
| makeCombinedPrediction | Combine classifier and CAGE data, for final prediction table |
| makeORFPredictionData | Predict table for uORFs |
| makeTrainingAndPredictionData | All features from sequence, Riboseq and RNAseq |
| makeTrainingData | Get CDS and 3'UTR TrainingData of ribo seq features |
| matchByTranscript | Takes two tables from the database and extracts the rows of... |
| p | shortcut for paste0() |
| pcaCAGEValidation | validate features using seperate them using pca and quantiles |
| perSampleCountPlot | Per sample library plot overall counts |
| predictionVsCageHits | Plot top tissues |
| predictUorfs | Predict uORFs using random forrest classification |
| readTable | Read a table from the database |
| removeIDColumns | Remove non numberic columns on left side |
| sequenceClassifier | Alternative ORF sequence classifier |
| startAndStopCodonPlots | Distribution of start and stop codon according to total... |
| startCodonMetrics | Get start codon bias usage |
| strongCDS | Find active CDS |
| subset.ORF | Subset orfs by filters given |
| tableNotExists | Does table exist |
| test.artificial | Test artificial vs original cds |
| toGRFromUniqueID | Create GRangesList of ORF IDs |
| trainClassifier | The training model with cds and 3' UTRs as random forest |
| validateExperiments | Validate uorfs of data-base |
| validateInputs | Validation of experiments |
| validateStartCodons | check that all orfs acctually have a valid start codon A good... |
| varianceTissueUsage | Venn diagram between two tissues |
| venn.diagram.uORFs | venn diagram of uORFs |
| verification.conf.matrix | Get comparison of validation model to full CDS length |
| weakTrailer | Find non-active trailers |
