API for Roleren/ORFik
Open Reading Frames in Genomics
| Global functions | |
|---|---|
| DEG.analysis | Man page Source code |
| DEG.plot.static | Man page Source code |
| DEG_DESeq | Source code |
| DEG_design | Source code |
| DEG_input_validation | Source code |
| DEG_model | Man page Source code |
| DEG_model_results | Man page Source code |
| DEG_model_simple | Man page Source code |
| DTEG.analysis | Man page Source code |
| DTEG.plot | Man page Source code |
| DTEG_input_validation | Source code |
| DTEG_model_results | Source code |
| ORFik | Man page |
| ORFik-package | Man page |
| ORFik.template.experiment | Man page Source code |
| ORFik.template.experiment.zf | Man page Source code |
| ORFikQC | Man page |
| QC_count_tables | Man page Source code |
| QCfolder | Man page |
| QCfolder,experiment-method | Man page |
| QCplots | Man page Source code |
| QCreport | Man page Source code |
| QCstats | Man page Source code |
| QCstats.plot | Man page Source code |
| RiboQC.plot | Man page |
| SRP_from_GSE | Source code |
| STAR.align.folder | Man page Source code |
| STAR.align.single | Man page Source code |
| STAR.allsteps.multiQC | Man page Source code |
| STAR.index | Man page Source code |
| STAR.install | Man page Source code |
| STAR.multiQC | Man page Source code |
| STAR.remove.crashed.genome | Man page Source code |
| TOP.Motif.ecdf | Man page |
| abstract_save | Source code |
| addCdsOnLeaderEnds | Man page Source code |
| addNewTSSOnLeaders | Man page Source code |
| add_author | Source code |
| add_pubmed_id | Source code |
| alignmentFeatureStatistics | Man page Source code |
| allFeaturesHelper | Man page Source code |
| appendZeroes | Man page |
| artificial.orfs | Man page Source code |
| asTX | Man page Source code |
| assignAnnotations | Man page |
| assignFirstExonsStartSite | Man page Source code |
| assignLastExonsStopSite | Man page Source code |
| assignTSSByCage | Man page Source code |
| auto_detect_gtf_in_dir | Source code |
| bamVarName | Man page Source code |
| bamVarNamePicker | Man page Source code |
| batchNames | Man page Source code |
| bedToGR | Man page Source code |
| browseSRA | Man page Source code |
| categorize_ORFs | Source code |
| categorize_and_filter_ORFs | Source code |
| cellLineNames | Man page Source code |
| cellTypeNames | Man page Source code |
| changePointAnalysis | Man page Source code |
| checkRFP | Man page Source code |
| checkRNA | Man page Source code |
| codonSumsPerGroup | Man page Source code |
| codon_usage | Man page |
| codon_usage_exp | Man page |
| codon_usage_plot | Man page |
| collapse.by.scores | Man page Source code |
| collapse.fastq | Man page Source code |
| collapse.fastq.internal | Source code |
| collapseDuplicatedReads | Man page |
| collapseDuplicatedReads,GAlignmentPairs-method | Man page |
| collapseDuplicatedReads,GAlignments-method | Man page |
| collapseDuplicatedReads,GRanges-method | Man page |
| collapseDuplicatedReads,data.table-method | Man page |
| combn.pairs | Man page |
| computeFeatures | Man page Source code |
| computeFeaturesCage | Man page Source code |
| conditionNames | Man page Source code |
| config | Man page Source code |
| config.exper | Man page Source code |
| config.save | Man page Source code |
| config_file | Man page Source code |
| contaminants_download | Source code |
| contaminants_processing | Source code |
| convertLibs | Man page Source code |
| convertToOneBasedRanges | Man page Source code |
| convert_bam_to_ofst | Man page Source code |
| convert_to_bigWig | Man page Source code |
| convert_to_covRle | Man page Source code |
| convert_to_covRleList | Man page Source code |
| convert_to_fstWig | Man page Source code |
| cor_plot | Man page |
| cor_table | Man page |
| correlation.plots | Man page |
| countOverlapsW | Man page Source code |
| countTable | Man page Source code |
| countTable_regions | Man page Source code |
| covRle | Man page Source code |
| covRle-class | Man page |
| covRleFromGR | Man page Source code |
| covRleList | Man page Source code |
| covRleList-class | Man page |
| coverageByTranscriptC | Man page |
| coverageByTranscriptW | Man page |
| coverageGroupings | Man page |
| coverageHeatMap | Man page Source code |
| coveragePerORFStatistics | Source code |
| coveragePerTiling | Man page |
| coverageScorings | Man page |
| coverage_to_dt | Man page |
| create.experiment | Man page Source code |
| defineIsoform | Man page |
| defineTrailer | Man page Source code |
| design,experiment-method | Man page |
| detectRibosomeShifts | Man page Source code |
| detect_ribo_orfs | Man page |
| disengagementScore | Man page |
| distToCds | Man page Source code |
| distToTSS | Man page Source code |
| download.SRA | Man page Source code |
| download.SRA.metadata | Man page Source code |
| download.ebi | Man page Source code |
| downstreamFromPerGroup | Man page Source code |
| downstreamN | Man page Source code |
| downstreamOfPerGroup | Man page Source code |
| entropy | Man page Source code |
| envExp | Man page |
| envExp,experiment-method | Man page |
| envExp<- | Man page |
| envExp<-,experiment-method | Man page |
| exists.ftp.dir.fast | Man page |
| exists.ftp.file.fast | Man page |
| experiment | Man page |
| experiment-class | Man page |
| experiment.colors | Man page Source code |
| experiment_parse_list_info | Source code |
| export.bed12 | Man page Source code |
| export.bedo | Man page Source code |
| export.bedoc | Man page Source code |
| export.bigWig | Man page Source code |
| export.cov | Source code |
| export.covlist | Source code |
| export.fstwig | Man page Source code |
| export.ofst | Man page |
| export.ofst,GAlignmentPairs-method | Man page |
| export.ofst,GAlignments-method | Man page |
| export.ofst,GRanges-method | Man page |
| export.wiggle | Man page Source code |
| extendLeaders | Man page Source code |
| extendTrailers | Man page Source code |
| extendsTSSexons | Man page Source code |
| extract_run_id | Man page Source code |
| f | Man page |
| f,covRle-method | Man page |
| fetch_xml_attributes | Source code |
| filepath | Man page Source code |
| filepath_errors | Source code |
| filterCage | Man page Source code |
| filterExtremePeakGenes | Man page Source code |
| filterTranscripts | Man page |
| filterUORFs | Man page Source code |
| filter_empty_runs | Source code |
| fimport | Man page Source code |
| findFa | Man page Source code |
| findFromPath | Man page Source code |
| findLibrariesInFolder | Man page Source code |
| findMapORFs | Man page Source code |
| findMaxPeaks | Man page Source code |
| findNGSPairs | Man page Source code |
| findNewTSS | Man page Source code |
| findORFs | Man page Source code |
| findORFsFasta | Man page Source code |
| findORFs_fasta | Source code |
| findPeaksPerGene | Man page |
| findUORFs | Man page Source code |
| findUORFs_exp | Man page Source code |
| find_url_ebi | Man page Source code |
| find_url_ebi_safe | Man page Source code |
| firstEndPerGroup | Man page Source code |
| firstExonPerGroup | Man page Source code |
| firstStartPerGroup | Man page Source code |
| fix_malformed_gff | Man page Source code |
| flankPerGroup | Man page Source code |
| floss | Man page |
| footprints.analysis | Man page Source code |
| fpkm | Man page Source code |
| fpkm_calc | Man page Source code |
| fractionLength | Man page Source code |
| fractionNames | Man page Source code |
| fread.bed | Man page Source code |
| gSort | Man page Source code |
| gcContent | Man page Source code |
| geneToSymbol | Man page |
| getGAlignments | Man page Source code |
| getGAlignmentsPairs | Man page Source code |
| getGRanges | Man page Source code |
| getGenomeAndAnnotation | Man page Source code |
| getGtfPathFromTxdb | Man page |
| getNGenesCoverage | Man page |
| getWeights | Man page Source code |
| get_bioproject_candidates | Man page Source code |
| get_genome_fasta | Man page Source code |
| get_genome_gtf | Man page Source code |
| get_noncoding_rna | Man page Source code |
| get_phix_genome | Man page Source code |
| get_rRNA | Source code |
| get_silva_rRNA | Man page Source code |
| get_tRNA | Source code |
| groupGRangesBy | Man page Source code |
| groupings | Man page |
| hasHits | Man page Source code |
| heatMapL | Man page Source code |
| heatMapRegion | Man page Source code |
| heatMap_single | Man page Source code |
| import.bedo | Man page Source code |
| import.bedoc | Man page Source code |
| import.fstwig | Man page Source code |
| import.ofst | Man page Source code |
| importGtfFromTxdb | Man page |
| inhibitorNames | Man page Source code |
| initiationScore | Man page |
| insideOutsideORF | Man page |
| install.fastp | Man page Source code |
| install.sratoolkit | Man page Source code |
| is.ORF | Man page Source code |
| is.gr_or_grl | Man page Source code |
| is.grl | Man page Source code |
| is.range | Man page Source code |
| isInFrame | Man page Source code |
| isOverlapping | Man page Source code |
| isPeriodic | Man page Source code |
| kozakHeatmap | Man page Source code |
| kozakSequenceScore | Man page Source code |
| kozak_IR_ranking | Man page |
| lastExonEndPerGroup | Man page Source code |
| lastExonPerGroup | Man page Source code |
| lastExonStartPerGroup | Man page Source code |
| length,covRle-method | Man page |
| length,covRleList-method | Man page |
| lengths,covRle-method | Man page |
| lengths,covRleList-method | Man page |
| libFolder | Man page |
| libFolder,experiment-method | Man page |
| libNames | Man page Source code |
| libraryTypes | Man page Source code |
| list.experiments | Man page Source code |
| list.genomes | Man page Source code |
| loadRegion | Man page |
| loadRegions | Man page |
| loadTranscriptType | Man page |
| loadTxdb | Man page |
| longestORFs | Man page Source code |
| mainNames | Man page Source code |
| makeExonRanks | Man page Source code |
| makeORFNames | Man page Source code |
| makeSummarizedExperimentFromBam | Man page Source code |
| makeTxdbFromGenome | Man page Source code |
| mapToGRanges | Man page Source code |
| matchColors | Man page Source code |
| matchNaming | Man page Source code |
| matchSeqStyle | Man page |
| mergeFastq | Man page Source code |
| mergeLibs | Man page Source code |
| metaWindow | Man page Source code |
| metadata.autnaming | Man page Source code |
| metadata_count_table | Source code |
| model.matrix,experiment-method | Man page |
| name | Man page |
| name,experiment-method | Man page |
| name_decider | Source code |
| nrow,experiment-method | Man page |
| numCodons | Man page |
| numExonsPerGroup | Man page Source code |
| ofst_merge | Man page |
| optimizeReads | Man page |
| optimizedTranscriptLengths | Man page |
| optimized_txdb_path | Man page |
| orfFrameDistributions | Man page Source code |
| orfID | Man page Source code |
| orfScore | Man page |
| orfs_as_IRanges | Source code |
| orfs_as_List | Source code |
| organism,experiment-method | Man page |
| outputLibs | Man page Source code |
| pSitePlot | Man page Source code |
| pasteDir | Man page Source code |
| pcaExperiment | Man page |
| percentage_to_ratio | Man page Source code |
| plotHelper | Man page Source code |
| pmapFromTranscriptF | Man page Source code |
| pmapFromTranscriptsCPP | Source code |
| pmapToTranscriptF | Man page Source code |
| pmapToTranscriptsCPP | Source code |
| prettyScoring | Man page Source code |
| pseudo.transform | Man page |
| pshifts_export | Source code |
| r | Man page |
| r,covRle-method | Man page |
| rankOrder | Man page Source code |
| read.experiment | Man page Source code |
| readBam | Man page Source code |
| readBigWig | Man page Source code |
| readLengthTable | Man page Source code |
| readWidths | Man page Source code |
| readWig | Man page Source code |
| reassignTSSbyCage | Man page Source code |
| reassignTxDbByCage | Man page Source code |
| reduceKeepAttr | Man page Source code |
| regionPerReadLength | Man page |
| remakeTxdbExonIds | Man page Source code |
| remove.experiments | Man page Source code |
| remove.file_ext | Man page |
| removeMetaCols | Man page |
| removeORFsWithSameStartAsCDS | Man page Source code |
| removeORFsWithSameStopAsCDS | Man page Source code |
| removeORFsWithStartInsideCDS | Man page Source code |
| removeORFsWithinCDS | Man page Source code |
| removeTxdbExons | Man page |
| removeTxdbTranscripts | Man page |
| rename.SRA.files | Man page Source code |
| repNames | Man page Source code |
| resFolder | Man page |
| resFolder,experiment-method | Man page |
| restrictTSSByUpstreamLeader | Man page Source code |
| revElementsF | Man page |
| reverseMinusStrandPerGroup | Man page Source code |
| riboORFs | Man page |
| riboORFsFolder | Man page |
| ribo_fft | Man page Source code |
| ribo_fft_plot | Man page Source code |
| ribosomeReleaseScore | Man page |
| ribosomeStallingScore | Man page |
| rnaNormalize | Man page Source code |
| runIDs | Man page |
| runIDs,experiment-method | Man page |
| sample_info_append_SRA | Source code |
| sample_info_download | Source code |
| sample_info_single | Source code |
| save.experiment | Man page Source code |
| save.fstwig | Source code |
| savePlot | Man page Source code |
| scaledWindowPositions | Man page Source code |
| scoreSummarizedExperiment | Man page Source code |
| seq_usage | Source code |
| seqinfo,covRle-method | Man page |
| seqinfo,covRleList-method | Man page |
| seqinfo,experiment-method | Man page |
| seqlevels,covRle-method | Man page |
| seqlevels,covRleList-method | Man page |
| seqlevels,experiment-method | Man page |
| seqnamesPerGroup | Man page Source code |
| shiftFootprints | Man page Source code |
| shiftFootprintsByExperiment | Man page |
| shiftPlots | Man page |
| shift_narrow | Source code |
| shifts.load | Man page Source code |
| show,covRle-method | Man page |
| show,covRleList-method | Man page |
| show,experiment-method | Man page |
| simpleLibs | Man page |
| sortPerGroup | Man page Source code |
| splitIn3Tx | Man page Source code |
| stageNames | Man page Source code |
| startCodons | Man page Source code |
| startDefinition | Man page Source code |
| startRegion | Man page Source code |
| startRegionCoverage | Man page |
| startRegionString | Man page Source code |
| startSites | Man page Source code |
| stopCodons | Man page Source code |
| stopDefinition | Man page Source code |
| stopRegion | Man page Source code |
| stopSites | Man page Source code |
| strandBool | Man page Source code |
| strandMode,covRle-method | Man page |
| strandMode,covRleList-method | Man page |
| strandPerGroup | Man page Source code |
| study_runinfo_download_deprecated | Source code |
| subsetCoverage | Man page Source code |
| subsetToFrame | Man page Source code |
| subset_count_table | Source code |
| symbols | Man page |
| symbols,experiment-method | Man page |
| te.plot | Man page Source code |
| te.table | Man page Source code |
| te_rna.plot | Man page Source code |
| tile1 | Man page Source code |
| tissueNames | Man page Source code |
| topMotif | Man page Source code |
| transcriptWindow | Man page Source code |
| transcriptWindow1 | Man page Source code |
| transcriptWindowPer | Man page Source code |
| translationalEff | Man page |
| trim_detection | Man page |
| trim_detection_message | Source code |
| trimming.table | Man page Source code |
| txNames | Man page Source code |
| txNamesToGeneNames | Man page |
| txSeqsFromFa | Man page Source code |
| uORFSearchSpace | Man page Source code |
| uniqueGroups | Man page Source code |
| uniqueOrder | Man page Source code |
| unlistGrl | Man page |
| updateTxdbRanks | Man page |
| updateTxdbStartSites | Man page |
| upstreamFromPerGroup | Man page Source code |
| upstreamOfPerGroup | Man page Source code |
| validGRL | Man page Source code |
| validSeqlevels | Man page Source code |
| validateExperiments | Man page Source code |
| widthPerGroup | Man page Source code |
| windowCoveragePlot | Man page Source code |
| windowPerGroup | Man page Source code |
| windowPerReadLength | Man page |
| windowPerTranscript | Man page Source code |
| xAxisScaler | Man page Source code |
| yAxisScaler | Man page Source code |
