Files in JokingHero/ORFik

Open Reading Frames in Genomics

R/Dif_expression_Analysis.R R/Dif_expression_helpers.R R/Dif_expression_plots.R R/ORFik.R R/ORFs_annotations.R R/ORFs_helpers.R R/RcppExports.R R/RiboORFs_detect_and_classify.R R/SRA_Entrez_API.R R/SRA_helper.R R/SRA_metadata.R R/STAR.R R/STAR_multiQC.R R/SummarizedExperiment_helpers.R R/cage_annotations.R R/codon_usage.R R/compute_Features.R R/covRLE_class.R R/coverage_filters.R R/coverage_heatmaps.R R/coverage_helpers.R R/coverage_plots.R R/experiment.R R/experiment_IO.R R/experiment_class.R R/experiment_files.R R/experiment_naming.R R/experiment_plots.R R/fastq_helpers.R R/feature_helpers.R R/find_ORFs.R R/general_plots.R R/genome_download.R R/genome_download_helper.R R/gr_helpers.R R/gr_or_grl_helpers.R R/gr_positions.R R/grl_extend.R R/grl_helpers.R R/grl_region.R R/ranges_helpers.R R/report.R R/report_helpers.R R/report_plots.R R/riboseq_features.R R/sequence_features.R R/shift_footprints.R R/shift_footprints_helpers.R R/txdbHelpers.R R/uORF_helpers.R R/utils.R R/utils_collapse.R R/utils_directory_config.R R/utils_exports.R R/utils_format_conversion.R R/utils_imports.R R/validity.R README.md inst/extdata/Homo_sapiens_sample/QC_STATS/DTEG_plot.pdf man/DEG.analysis.Rd man/DEG.plot.static.Rd man/DEG_model.Rd man/DEG_model_results.Rd man/DEG_model_simple.Rd man/DTEG.analysis.Rd man/DTEG.plot.Rd man/ORFik-package.Rd man/ORFik.template.experiment.Rd man/ORFik.template.experiment.zf.Rd man/ORFikQC.Rd man/QC_count_tables.Rd man/QCfolder-experiment-method.Rd man/QCfolder.Rd man/QCplots.Rd man/QCreport.Rd man/QCstats.Rd man/QCstats.plot.Rd man/RiboQC.plot.Rd man/STAR.align.folder.Rd man/STAR.align.single.Rd man/STAR.allsteps.multiQC.Rd man/STAR.index.Rd man/STAR.install.Rd man/STAR.multiQC.Rd man/STAR.remove.crashed.genome.Rd man/TOP.Motif.ecdf.Rd man/addCdsOnLeaderEnds.Rd man/addNewTSSOnLeaders.Rd man/add_pseudo_5utrs_txdb_if_needed.Rd man/alignmentFeatureStatistics.Rd man/allFeaturesHelper.Rd man/appendZeroes.Rd man/artificial.orfs.Rd man/asTX.Rd man/assignAnnotations.Rd man/assignFirstExonsStartSite.Rd man/assignLastExonsStopSite.Rd man/assignTSSByCage.Rd man/bamVarName.Rd man/bamVarNamePicker.Rd man/batchNames.Rd man/bedToGR.Rd man/browseSRA.Rd man/cellLineNames.Rd man/cellTypeNames.Rd man/changePointAnalysis.Rd man/checkRFP.Rd man/checkRNA.Rd man/codonSumsPerGroup.Rd man/codon_usage.Rd man/codon_usage_exp.Rd man/codon_usage_plot.Rd man/collapse.by.scores.Rd man/collapse.fastq.Rd man/collapseDuplicatedReads-GAlignmentPairs-method.Rd man/collapseDuplicatedReads-GAlignments-method.Rd man/collapseDuplicatedReads-GRanges-method.Rd man/collapseDuplicatedReads-data.table-method.Rd man/collapseDuplicatedReads.Rd man/combn.pairs.Rd man/computeFeatures.Rd man/computeFeaturesCage.Rd man/conditionNames.Rd man/config.Rd man/config.exper.Rd man/config.save.Rd man/config_file.Rd man/convertLibs.Rd man/convertToOneBasedRanges.Rd man/convert_bam_to_ofst.Rd man/convert_to_bigWig.Rd man/convert_to_covRle.Rd man/convert_to_covRleList.Rd man/convert_to_fstWig.Rd man/cor_plot.Rd man/cor_table.Rd man/correlation.plots.Rd man/countOverlapsW.Rd man/countTable.Rd man/countTable_regions.Rd man/covRle-class.Rd man/covRle.Rd man/covRleFromGR.Rd man/covRleList-class.Rd man/covRleList.Rd man/coverageByTranscriptC.Rd man/coverageByTranscriptW.Rd man/coverageGroupings.Rd man/coverageHeatMap.Rd man/coveragePerTiling.Rd man/coverageScorings.Rd man/coverage_to_dt.Rd man/create.experiment.Rd man/defineIsoform.Rd man/defineTrailer.Rd man/design-experiment-method.Rd man/detectRibosomeShifts.Rd man/detect_ribo_orfs.Rd man/disengagementScore.Rd man/distToCds.Rd man/distToTSS.Rd man/distanceToFollowing.Rd man/distanceToPreceding.Rd man/download.SRA.Rd man/download.SRA.metadata.Rd man/download.ebi.Rd man/downstreamFromPerGroup.Rd man/downstreamN.Rd man/downstreamOfPerGroup.Rd man/entropy.Rd man/envExp-experiment-method.Rd man/envExp-set-experiment-method.Rd man/envExp-set.Rd man/envExp.Rd man/exists.ftp.dir.fast.Rd man/exists.ftp.file.fast.Rd man/experiment-class.Rd man/experiment.colors.Rd man/export.bed12.Rd man/export.bedo.Rd man/export.bedoc.Rd man/export.bigWig.Rd man/export.fstwig.Rd man/export.ofst-GAlignmentPairs-method.Rd man/export.ofst-GAlignments-method.Rd man/export.ofst-GRanges-method.Rd man/export.ofst.Rd man/export.wiggle.Rd man/extendLeaders.Rd man/extendLeadersUntil.Rd man/extendTrailers.Rd man/extendTrailersUntil.Rd man/extendsTSSexons.Rd man/extract_run_id.Rd man/f-covRle-method.Rd man/f.Rd man/file_ext_without_compression.Rd man/filepath.Rd man/filterCage.Rd man/filterExtremePeakGenes.Rd man/filterTranscripts.Rd man/filterUORFs.Rd man/fimport.Rd man/findFa.Rd man/findFromPath.Rd man/findLibrariesInFolder.Rd man/findMapORFs.Rd man/findMaxPeaks.Rd man/findNGSPairs.Rd man/findNewTSS.Rd man/findORFs.Rd man/findORFsFasta.Rd man/findPeaksPerGene.Rd man/findUORFs.Rd man/findUORFs_exp.Rd man/find_url_ebi.Rd man/find_url_ebi_safe.Rd man/firstEndPerGroup.Rd man/firstExonPerGroup.Rd man/firstStartPerGroup.Rd man/fix_malformed_gff.Rd man/flankPerGroup.Rd man/floss.Rd man/footprints.analysis.Rd man/fpkm.Rd man/fpkm_calc.Rd man/fractionLength.Rd man/fractionNames.Rd man/fread.bed.Rd man/gSort.Rd man/gcContent.Rd man/geneToSymbol.Rd man/getGAlignments.Rd man/getGAlignmentsPairs.Rd man/getGRanges.Rd man/getGenomeAndAnnotation.Rd man/getGtfPathFromTxdb.Rd man/getNGenesCoverage.Rd man/getWeights.Rd man/get_bioproject_candidates.Rd man/get_genome_fasta.Rd man/get_genome_gtf.Rd man/get_noncoding_rna.Rd man/get_phix_genome.Rd man/get_silva_rRNA.Rd man/groupGRangesBy.Rd man/groupings.Rd man/hasHits.Rd man/heatMapL.Rd man/heatMapRegion.Rd man/heatMap_single.Rd man/import.bedo.Rd man/import.bedoc.Rd man/import.fstwig.Rd man/import.ofst.Rd man/importGtfFromTxdb.Rd man/inhibitorNames.Rd man/initiationScore.Rd man/insideOutsideORF.Rd man/install.fastp.Rd man/install.sratoolkit.Rd man/is.ORF.Rd man/is.gr_or_grl.Rd man/is.grl.Rd man/is.range.Rd man/isInFrame.Rd man/isOverlapping.Rd man/isPeriodic.Rd man/kozakHeatmap.Rd man/kozakSequenceScore.Rd man/kozak_IR_ranking.Rd man/lastExonEndPerGroup.Rd man/lastExonPerGroup.Rd man/lastExonStartPerGroup.Rd man/length-covRle-method.Rd man/length-covRleList-method.Rd man/lengths-covRle-method.Rd man/lengths-covRleList-method.Rd man/libFolder-experiment-method.Rd man/libFolder.Rd man/libNames.Rd man/libraryTypes.Rd man/list.experiments.Rd man/list.genomes.Rd man/loadRegion.Rd man/loadRegions.Rd man/loadTranscriptType.Rd man/loadTxdb.Rd man/longestORFs.Rd man/mainNames.Rd man/makeExonRanks.Rd man/makeORFNames.Rd man/makeSummarizedExperimentFromBam.Rd man/makeTxdbFromGenome.Rd man/mapToGRanges.Rd man/matchColors.Rd man/matchNaming.Rd man/matchSeqStyle.Rd man/mergeFastq.Rd man/mergeLibs.Rd man/metaWindow.Rd man/metadata.autnaming.Rd man/model.matrix-experiment-method.Rd man/name-experiment-method.Rd man/name.Rd man/nrow-experiment-method.Rd man/numCodons.Rd man/numExonsPerGroup.Rd man/ofst_merge.Rd man/optimizeReads.Rd man/optimizeTranscriptRegions.Rd man/optimizedTranscriptLengths.Rd man/optimized_txdb_path.Rd man/orfFrameDistributions.Rd man/orfID.Rd man/orfScore.Rd man/organism-experiment-method.Rd man/outputLibs.Rd man/pSitePlot.Rd man/pasteDir.Rd man/pcaExperiment.Rd man/percentage_to_ratio.Rd man/plotHelper.Rd man/pmapFromTranscriptF.Rd man/pmapToTranscriptF.Rd man/prettyScoring.Rd man/pseudo.transform.Rd man/r-covRle-method.Rd man/r.Rd man/rankOrder.Rd man/read.experiment.Rd man/readBam.Rd man/readBigWig.Rd man/readLengthTable.Rd man/readWidths.Rd man/readWig.Rd man/reassignTSSbyCage.Rd man/reassignTxDbByCage.Rd man/reduceKeepAttr.Rd man/regionPerReadLength.Rd man/remakeTxdbExonIds.Rd man/remove.experiments.Rd man/remove.file_ext.Rd man/removeMetaCols.Rd man/removeORFsWithSameStartAsCDS.Rd man/removeORFsWithSameStopAsCDS.Rd man/removeORFsWithStartInsideCDS.Rd man/removeORFsWithinCDS.Rd man/removeTxdbExons.Rd man/removeTxdbTranscripts.Rd man/rename.SRA.files.Rd man/repNames.Rd man/resFolder-experiment-method.Rd man/resFolder.Rd man/restrictTSSByUpstreamLeader.Rd man/revElementsF.Rd man/reverseMinusStrandPerGroup.Rd man/riboORFs.Rd man/riboORFsFolder.Rd man/ribo_fft.Rd man/ribo_fft_plot.Rd man/ribosomeReleaseScore.Rd man/ribosomeStallingScore.Rd man/rnaNormalize.Rd man/runIDs-experiment-method.Rd man/runIDs.Rd man/save.experiment.Rd man/savePlot.Rd man/scaledWindowPositions.Rd man/scoreSummarizedExperiment.Rd man/seqinfo-covRle-method.Rd man/seqinfo-covRleList-method.Rd man/seqinfo-experiment-method.Rd man/seqlevels-covRle-method.Rd man/seqlevels-covRleList-method.Rd man/seqlevels-experiment-method.Rd man/seqnames-experiment-method.Rd man/seqnamesPerGroup.Rd man/shiftFootprints.Rd man/shiftFootprintsByExperiment.Rd man/shiftPlots.Rd man/shifts_load.Rd man/shifts_save.Rd man/show-covRle-method.Rd man/show-covRleList-method.Rd man/show-experiment-method.Rd man/simpleLibs.Rd man/sortPerGroup.Rd man/splitIn3Tx.Rd man/stageNames.Rd man/startCodons.Rd man/startDefinition.Rd man/startRegion.Rd man/startRegionCoverage.Rd man/startRegionString.Rd man/startSites.Rd man/stopCodons.Rd man/stopDefinition.Rd man/stopRegion.Rd man/stopSites.Rd man/strandBool.Rd man/strandMode-covRle-method.Rd man/strandMode-covRleList-method.Rd man/strandPerGroup.Rd man/subsetCoverage.Rd man/subsetToFrame.Rd man/sum-covRle-method.Rd man/symbols-experiment-method.Rd man/symbols.Rd man/te.plot.Rd man/te.table.Rd man/te_rna.plot.Rd man/tile1.Rd man/tissueNames.Rd man/topMotif.Rd man/transcriptWindow.Rd man/transcriptWindow1.Rd man/transcriptWindowPer.Rd man/translationalEff.Rd man/trim_detection.Rd man/trimming.table.Rd man/txNames.Rd man/txNamesToGeneNames.Rd man/txSeqsFromFa.Rd man/uORFSearchSpace.Rd man/uniqueGroups.Rd man/uniqueOrder.Rd man/unlistGrl.Rd man/unlistToExtremities.Rd man/updateTxdbRanks.Rd man/updateTxdbStartSites.Rd man/upstreamFromPerGroup.Rd man/upstreamOfPerGroup.Rd man/validGRL.Rd man/validSeqlevels.Rd man/validateExperiments.Rd man/widthPerGroup.Rd man/windowCoveragePlot.Rd man/windowPerGroup.Rd man/windowPerReadLength.Rd man/windowPerTranscript.Rd man/xAxisScaler.Rd man/yAxisScaler.Rd tests/testthat.R tests/testthat/test_DEG.R tests/testthat/test_ORFs_helpers.R tests/testthat/test_cage.R tests/testthat/test_cds_helpers.R tests/testthat/test_covRle.R tests/testthat/test_coverage.R tests/testthat/test_experiment.R tests/testthat/test_features.R tests/testthat/test_granges_helpers.R tests/testthat/test_import.R tests/testthat/test_report.R tests/testthat/test_shift_footprints.R tests/testthat/test_utils.R vignettes/Annotation_Alignment.Rmd vignettes/Importing_Data.Rmd vignettes/ORFikExperiment.Rmd vignettes/ORFikOverview.Rmd vignettes/Ribo-seq_pipeline.Rmd vignettes/Working_with_transcripts.Rmd