{ "_id": "6a1ac1651d7bb097a09d84c9", "Package": "ORFik", "Type": "Package", "Title": "Open Reading Frames in Genomics", "Version": "1.33.0", "Encoding": "UTF-8", "Authors@R": "c(\nperson(given = \"Haakon\", family = \"Tjeldnes\", email = \"hauken_heyken@hotmail.com\", role = c(\"aut\", \"cre\", \"dtc\"),\ncomment = c(ORCID = \"0000-0002-2077-747X\")),\nperson(given = \"Kornel\", family = \"Labun\", email = \"kornellabun@gmail.com\", role = c(\"aut\", \"cph\")),\nperson(given = \"Michal\", family = \"Swirski\", email = \"michal.swirski@uw.edu.pl\", role = c(\"ctb\")),\nperson(given = \"Katarzyna\", family = \"Chyzynska\", email = \"katchyz@gmail.com\", role = c(\"ctb\", \"dtc\")),\nperson(given = \"Yamila\", family = \"Torres Cleuren\", email = \"yamilatorrescleuren@gmail.com\", role = c(\"ctb\", \"ths\")),\nperson(given = \"Eivind\", family = \"Valen\", email = \"eivind.valen@gmail.com\", role = c(\"ths\", \"fnd\")))", "Description": "R package for analysis of transcript and translation\nfeatures through manipulation of sequence data and NGS data\nlike Ribo-Seq, RNA-Seq, TCP-Seq and CAGE. It is generalized in\nthe sense that any transcript region can be analysed, as the\nname hints to it was made with investigation of ribosomal\npatterns over Open Reading Frames (ORFs) as it's primary use\ncase. ORFik is extremely fast through use of C++, data.table\nand GenomicRanges. Package allows to reassign starts of the\ntranscripts with the use of CAGE-Seq data, automatic shifting\nof RiboSeq reads, finding of Open Reading Frames for whole\ngenomes and much more.", "biocViews": "ImmunoOncology, Software, Sequencing, RiboSeq, RNASeq,\nFunctionalGenomics, Coverage, Alignment, DataImport", "License": "MIT + file LICENSE", "BugReports": "https://github.com/Roleren/ORFik/issues", "URL": "https://github.com/Roleren/ORFik", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nlibpng-dev libuv1-dev libxml2-dev libssl-dev libx11-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:47:59 UTC", "RemoteUrl": "https://github.com/bioc/ORFik", "RemoteRef": "HEAD", "RemoteSha": "bcf19ce8103042e4b1babe8e2399223f3dd45dc6", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-30 07:23:30 UTC", "User": "root" }, "Author": "Haakon Tjeldnes [aut, cre, dtc] 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"coverageByTranscriptW" ] }, { "page": "coverageHeatMap", "title": "Create a heatmap of coverage", "concept": [ "coveragePlot", "heatmaps" ], "topics": [ "coverageHeatMap" ] }, { "page": "coveragePerTiling", "title": "Get coverage per group", "concept": [ "ExtendGenomicRanges" ], "topics": [ "coveragePerTiling" ] }, { "page": "coverageScorings", "title": "Add a coverage scoring scheme", "concept": [ "coverage" ], "topics": [ "coverageScorings" ] }, { "page": "covRle", "title": "Coverage Rlelist for both strands", "concept": [ "covRLE" ], "topics": [ "covRle" ] }, { "page": "covRle-class", "title": "Coverage Rle for both strands or single", "concept": [ "covRLE" ], "topics": [ "covRle-class" ] }, { "page": "covRleFromGR", "title": "Convert GRanges to covRle", "concept": [ "covRLE" ], "topics": [ "covRleFromGR" ] }, { "page": "covRleList", "title": "Coverage Rlelist for both strands", "concept": [ "covRLE" ], "topics": [ "covRleList" ] }, { "page": "covRleList-class", "title": "List of covRle", "concept": [ "covRLE" ], "topics": [ "covRleList-class" ] }, { "page": "create.experiment", "title": "Create an ORFik 'experiment'", "concept": [ "ORFik_experiment" ], "topics": [ "create.experiment" ] }, { "page": "defineTrailer", "title": "Defines trailers for ORF.", "concept": [ "ORFHelpers" ], "topics": [ "defineTrailer" ] }, { "page": "DEG_gorilla", "title": "GO analysis with GOrilla", "concept": [ "GOrilla" ], "topics": [ "DEG_gorilla" ] }, { "page": "DEG_gorilla_copy_to_local", "title": "Copy GOrilla result htmls to local", "concept": [ "GOrilla" ], "topics": [ "DEG_gorilla_copy_to_local" ] }, { "page": "DEG_gorilla_local_load_data", "title": "Load all GOrilla xls files from study", "topics": [ "DEG_gorilla_local_load_data" ] }, { "page": "DEG_gorilla_plot", "title": "Plot GOrilla xls results", "topics": [ "DEG_gorilla_plot" ] }, { "page": "DEG_model", "title": "Get DESeq2 model without running results", "concept": [ "DifferentialExpression" ], "topics": [ "DEG_model" ] }, { "page": "DEG_model_results", "title": "Get DESeq2 model results from DESeqDataSet", "topics": [ "DEG_model_results" ] }, { "page": "DEG_model_simple", "title": "Simple Fpkm ratio test DEG", "topics": [ "DEG_model_simple" ] }, { "page": "DEG.analysis", "title": "Run differential TE analysis", "topics": [ "DEG.analysis" ] }, { "page": "DEG.plot.static", "title": "Plot DEG result", "concept": [ "DifferentialExpression" ], "topics": [ "DEG.plot.static" ] }, { "page": "design-experiment-method", "title": "Get experimental design Find the column/columns that create a separation between samples, by default skips replicate and choose first that is from either: libtype, condition, stage and fraction.", "topics": [ "design,experiment-method" ] }, { "page": "detect_drive", "title": "Detects the mounted drive based on a mounted path", "topics": [ "detect_drive" ] }, { "page": "detect_ribo_orfs", "title": "Detect ORFs by Ribosome profiling data", "topics": [ "detect_ribo_orfs" ] }, { "page": "detectRibosomeShifts", "title": "Detect ribosome shifts", "concept": [ "pshifting" ], "topics": [ "detectRibosomeShifts" ] }, { "page": "disengagementScore", "title": "Disengagement score (DS)", "concept": [ "features" ], "topics": [ "disengagementScore" ] }, { "page": "distanceToFollowing", "title": "Distance to following range group", "topics": [ "distanceToFollowing" ] }, { "page": "distanceToPreceding", "title": "Distance to preceding range group", "topics": [ "distanceToPreceding" ] }, { "page": "distToCds", "title": "Get distances between ORF ends and starts of their transcripts cds.", "concept": [ "features" ], "topics": [ "distToCds" ] }, { "page": "distToTSS", "title": "Get distances between ORF Start and TSS of its transcript", "concept": [ "features" ], "topics": [ "distToTSS" ] }, { "page": "download_gene_homologues", "title": "Download homologue information of a gene", "topics": [ "download_gene_homologues" ] }, { "page": "download_gene_info", "title": "Download summary information of a gene", "topics": [ "download_gene_info" ] }, { "page": "download.SRA", "title": "Download read libraries from SRA", "concept": [ "sra" ], "topics": [ "download.SRA" ] }, { "page": "download.SRA.metadata", "title": "Downloads metadata from SRA", "concept": [ "sra" ], "topics": [ "download.SRA.metadata" ] }, { "page": "DTEG.analysis", "title": "Run differential TE analysis", "concept": [ "DifferentialExpression" ], "topics": [ "DTEG.analysis" ] }, { "page": "DTEG.plot", "title": "Plot DTEG result", "concept": [ "DifferentialExpression" ], "topics": [ "DTEG.plot" ] }, { "page": "end-GRanges-method", "title": "Get ends of GRanges", "topics": [ "end,GRanges-method" ] }, { "page": "entropy", "title": "Percentage of maximum entropy", "concept": [ "features" ], "topics": [ "entropy" ] }, { "page": "envExp", "title": "Get ORFik experiment environment", "topics": [ "envExp" ] }, { "page": "envExp-experiment-method", "title": "Get ORFik experiment environment", "topics": [ "envExp,experiment-method" ] }, { "page": "envExp-set", "title": "Set ORFik experiment environment", "topics": [ "envExp<-" ] }, { "page": "envExp-set-experiment-method", "title": "Set ORFik experiment environment", "topics": [ "envExp<-,experiment-method" ] }, { "page": "exonsWithPseudoIntronsPerGroup", "title": "Get exons with pseudo introns per Group", "topics": [ "exonsWithPseudoIntronsPerGroup" ] }, { "page": "experiment-class", "title": "experiment class definition", "concept": [ "ORFik_experiment" ], "topics": [ "experiment", "experiment-class" ] }, { "page": "experiment.colors", "title": "Decide color for libraries by grouping", "topics": [ "experiment.colors" ] }, { "page": "export.bed12", "title": "Export as bed12 format", "concept": [ "utils" ], "topics": [ "export.bed12" ] }, { "page": "export.bedo", "title": "Store GRanges object as .bedo", "topics": [ "export.bedo" ] }, { "page": "export.bedoc", "title": "Store GAlignments object as .bedoc", "topics": [ "export.bedoc" ] }, { "page": "export.bigWig", "title": "Export as bigWig format", "concept": [ "utils" ], "topics": [ "export.bigWig" ] }, { "page": "export.fstwig", "title": "Export as fstwig (fastwig) format", "concept": [ "utils" ], "topics": [ "export.fstwig" ] }, { "page": "export.ofst", "title": "Store GRanges / GAlignments object as .ofst", "topics": [ "export.ofst" ] }, { "page": "export.ofst-data.frame-method", "title": "Store GRanges / GAlignments object as .ofst", "topics": [ "export.ofst,data.frame-method" ] }, { "page": "export.ofst-GAlignmentPairs-method", "title": "Store GRanges / GAlignments object as .ofst", "topics": [ "export.ofst,GAlignmentPairs-method" ] }, { "page": "export.ofst-GAlignments-method", "title": "Store GRanges / GAlignments object as .ofst", "topics": [ "export.ofst,GAlignments-method" ] }, { "page": "export.ofst-GRanges-method", "title": "Store GRanges / GAlignments object as .ofst", "topics": [ "export.ofst,GRanges-method" ] }, { "page": "export.wiggle", "title": "Export as wiggle format", "concept": [ "utils" ], "topics": [ "export.wiggle" ] }, { "page": "extendLeaders", "title": "Extend the leaders transcription start sites.", "concept": [ "ExtendGenomicRanges" ], "topics": [ "extendLeaders" ] }, { "page": "extendLeadersUntil", "title": "Extend Leaders Until", "topics": [ "extendLeadersUntil" ] }, { "page": "extendTrailers", "title": "Extend the Trailers transcription stop sites", "concept": [ "ExtendGenomicRanges" ], "topics": [ "extendTrailers" ] }, { "page": "extendTrailersUntil", "title": "Extend Trailers Until", "topics": [ "extendTrailersUntil" ] }, { "page": "extract_run_id", "title": "Extract SRR/ERR/DRR run IDs from string", "topics": [ "extract_run_id" ] }, { "page": "f", "title": "strandMode covRle", "topics": [ "f" ] }, { "page": "f-covRle-method", "title": "strandMode covRle", "topics": [ "f,covRle-method" ] }, { "page": "file_ext_without_compression", "title": "Get file extension of files without compressions", "topics": [ "file_ext_without_compression" ] }, { "page": "filepath", "title": "Get filepaths to ORFik experiment", "concept": [ "ORFik_experiment" ], "topics": [ "filepath" ] }, { "page": "filterExtremePeakGenes", "title": "Filter out transcript by a median filter", "topics": [ "filterExtremePeakGenes" ] }, { "page": "filterTranscripts", "title": "Filter transcripts by lengths", "topics": [ "filterTranscripts" ] }, { "page": "fimport", "title": "Load any type of sequencing reads", "concept": [ "utils" ], "topics": [ "fimport" ] }, { "page": "find_url_ebi", "title": "Locates and check if fastq files exists in ebi", "topics": [ "find_url_ebi" ] }, { "page": "findFa", "title": "Convenience wrapper for Rsamtools FaFile", "concept": [ "utils" ], "topics": [ "findFa" ] }, { "page": "findMapORFs", "title": "Find ORFs and immediately map them to their genomic positions.", "concept": [ "findORFs" ], "topics": [ "findMapORFs" ] }, { "page": "findORFs", "title": "Find Open Reading Frames.", "concept": [ "findORFs" ], "topics": [ "findORFs" ] }, { "page": "findORFsFasta", "title": "Finds Open Reading Frames in fasta files.", "concept": [ "findORFs" ], "topics": [ "findORFsFasta" ] }, { "page": "findPeaksPerGene", "title": "Find peaks per gene", "topics": [ "findPeaksPerGene" ] }, { "page": "findUORFs", "title": "Find upstream ORFs from transcript annotation", "concept": [ "findORFs" ], "topics": [ "findUORFs" ] }, { "page": "findUORFs_exp", "title": "Find upstream ORFs from transcript annotation", "topics": [ "findUORFs_exp" ] }, { "page": "firstEndPerGroup", "title": "Get first end per granges group", "topics": [ "firstEndPerGroup" ] }, { "page": "firstExonPerGroup", "title": "Get first exon per GRangesList group", "topics": [ "firstExonPerGroup" ] }, { "page": "firstStartPerGroup", "title": "Get first start per granges group", "topics": [ "firstStartPerGroup" ] }, { "page": "fix_malformed_gff", "title": "Fix a malformed gff file", "topics": [ "fix_malformed_gff" ] }, { "page": "flankPerGroup", "title": "Get flanks per group", "topics": [ "flankPerGroup" ] }, { "page": "floss", "title": "Fragment Length Organization Similarity Score", "concept": [ "features" ], "topics": [ "floss" ] }, { "page": "fpkm", "title": "Create normalizations of overlapping read counts.", "concept": [ "features" ], "topics": [ "fpkm" ] }, { "page": "fractionLength", "title": "Fraction Length", "concept": [ "features" ], "topics": [ "fractionLength" ] }, { "page": "fread.bed", "title": "Load bed file as GRanges", "concept": [ "utils" ], "topics": [ "fread.bed" ] }, { "page": "gcContent", "title": "Get GC content", "topics": [ "gcContent" ] }, { "page": "geneToSymbol", "title": "Get gene symbols from Ensembl gene ids", "topics": [ "geneToSymbol" ] }, { "page": "get_bioproject_candidates", "title": "Query eutils for bioproject IDs", "concept": [ "sra" ], "topics": [ "get_bioproject_candidates" ] }, { "page": "get_silva_rRNA", "title": "Download Silva SSU & LSU sequences", "topics": [ "get_silva_rRNA" ] }, { "page": "get_system_usage", "title": "System usage for Linux (Auto-detects correct drive if not provided)", "topics": [ "get_system_usage" ] }, { "page": "getGenomeAndAnnotation", "title": "Download genome (fasta), annotation (GTF) and contaminants", "concept": [ "STAR" ], "topics": [ "getGenomeAndAnnotation" ] }, { "page": "go_analaysis_gorilla", "title": "GO analysis with GOrilla", "topics": [ "go_analaysis_gorilla" ] }, { "page": "groupGRangesBy", "title": "Group GRanges", "topics": [ "groupGRangesBy" ] }, { "page": "groupings", "title": "Get number of ranges per group as an iteration", "topics": [ "groupings" ] }, { "page": "heatMap_single", "title": "Coverage heatmap of single libraries", "concept": [ "heatmaps" ], "topics": [ "heatMap_single" ] }, { "page": "heatMapRegion", "title": "Create coverage heatmaps of specified region", "concept": [ "heatmaps" ], "topics": [ "heatMapRegion" ] }, { "page": "import.bedo", "title": "Load GRanges object from .bedo", "topics": [ "import.bedo" ] }, { "page": "import.bedoc", "title": "Load GAlignments object from .bedoc", "topics": [ "import.bedoc" ] }, { "page": "import.fstwig", "title": "Import region from fastwig", "topics": [ "import.fstwig" ] }, { "page": "import.ofst", "title": "Load GRanges / GAlignments object from .ofst", "topics": [ "import.ofst" ] }, { "page": "importGtfFromTxdb", "title": "Import the GTF / GFF that made the txdb", "topics": [ "importGtfFromTxdb" ] }, { "page": "initiationScore", "title": "Get initiation score for a GRangesList of ORFs", "concept": [ "features" ], "topics": [ "initiationScore" ] }, { "page": "insideOutsideORF", "title": "Inside/Outside score (IO)", "concept": [ "features" ], "topics": [ "insideOutsideORF" ] }, { "page": "install.fastp", "title": "Download and prepare fastp trimmer", "concept": [ "STAR" ], "topics": [ "install.fastp" ] }, { "page": "install.sratoolkit", "title": "Download sra toolkit", "concept": [ "sra" ], "topics": [ "install.sratoolkit" ] }, { "page": "isInFrame", "title": "Find frame for each orf relative to cds", "concept": [ "features" ], "topics": [ "isInFrame" ] }, { "page": "isOverlapping", "title": "Find frame for each orf relative to cds", "concept": [ "features" ], "topics": [ "isOverlapping" ] }, { "page": "kozak_IR_ranking", "title": "Rank kozak initiation sequences", "topics": [ "kozak_IR_ranking" ] }, { "page": "kozakHeatmap", "title": "Make sequence region heatmap relative to scoring", "topics": [ "kozakHeatmap" ] }, { "page": "kozakSequenceScore", "title": "Make a score for each ORFs start region by proximity to Kozak", "concept": [ "features" ], "topics": [ "kozakSequenceScore" ] }, { "page": "lastExonEndPerGroup", "title": "Get last end per granges group", "topics": [ "lastExonEndPerGroup" ] }, { "page": "lastExonPerGroup", "title": "Get last exon per GRangesList group", "topics": [ "lastExonPerGroup" ] }, { "page": "lastExonStartPerGroup", "title": "Get last start per granges group", "topics": [ "lastExonStartPerGroup" ] }, { "page": "length-covRle-method", "title": "length covRle", "topics": [ "length,covRle-method" ] }, { "page": "length-covRleList-method", "title": "length covRleList", "topics": [ "length,covRleList-method" ] }, { "page": "length-GRangesList-method", "title": "Get length of GRangesList", "topics": [ "length,GRangesList-method" ] }, { "page": "lengths-covRle-method", "title": "lengths covRle", "topics": [ "lengths,covRle-method" ] }, { "page": "lengths-covRleList-method", "title": "lengths covRleList", "topics": [ "lengths,covRleList-method" ] }, { "page": "libFolder", "title": "Get path to ORFik experiment library folder", "topics": [ "libFolder" ] }, { "page": "libFolder-experiment-method", "title": "Get path to ORFik experiment library folder", "topics": [ "libFolder,experiment-method" ] }, { "page": "libraryTypes", "title": "Which type of library type in 'experiment'?", "concept": [ "ORFik_experiment" ], "topics": [ "libraryTypes" ] }, { "page": "list.experiments", "title": "List current experiment available", "topics": [ "list.experiments" ] }, { "page": "list.genomes", "title": "List genomes created with ORFik", "topics": [ "list.genomes" ] }, { "page": "loadRegion", "title": "Load transcript region", "topics": [ "loadRegion" ] }, { "page": "loadRegions", "title": "Get all regions of transcripts specified to environment", "topics": [ "loadRegions" ] }, { "page": "loadTranscriptType", "title": "Load transcripts of given biotype", "topics": [ "loadTranscriptType" ] }, { "page": "loadTxdb", "title": "General loader for txdb", "topics": [ "loadTxdb" ] }, { "page": "longestORFs", "title": "Get longest ORF per stop site", "concept": [ "ORFHelpers" ], "topics": [ "longestORFs" ] }, { "page": "makeGRangesFromDataFrameFast", "title": "Faster version (also less safe) of makeGRangesFromDataFrame", "topics": [ "makeGRangesFromDataFrameFast" ] }, { "page": "makeGRangesListFromCharacter", "title": "Convert a character vector to GRangesList", "topics": [ "makeGRangesListFromCharacter" ] }, { "page": "makeORFNames", "title": "Make ORF names per orf", "topics": [ "makeORFNames" ] }, { "page": "makeSummarizedExperimentFromBam", "title": "Make a count matrix from a library or experiment", "topics": [ "makeSummarizedExperimentFromBam" ] }, { "page": "makeSymbols", "title": "Make Gene symbols from txdb", "topics": [ "makeSymbols" ] }, { "page": "makeTxdbFromGenome", "title": "Make txdb from genome", "topics": [ "makeTxdbFromGenome" ] }, { "page": "mergeFastq", "title": "Merge groups of Fastq /Fasta files", "topics": [ "mergeFastq" ] }, { "page": "mergeLibs", "title": "Merge and save libraries of experiment", "topics": [ "mergeLibs" ] }, { "page": "metadata.autnaming", "title": "Guess SRA metadata columns", "topics": [ "metadata.autnaming" ] }, { "page": "metaWindow", "title": "Calculate meta-coverage of reads around input GRanges/List object.", "concept": [ "coverage" ], "topics": [ "metaWindow" ] }, { "page": "model.matrix-experiment-method", "title": "Get experiment design model matrix", "topics": [ "model.matrix,experiment-method" ] }, { "page": "name", "title": "Get name of ORFik experiment", "topics": [ "name" ] }, { "page": "name-experiment-method", "title": "Get name of ORFik experiment", "topics": [ "name,experiment-method" ] }, { "page": "names-GRangesList-method", "title": "Get names of GRangesList", "topics": [ "names,GRangesList-method" ] }, { "page": "names-set-GRangesList-method", "title": "Get names of GRangesList", "topics": [ "names<-,GRangesList-method" ] }, { "page": "nrow-experiment-method", "title": "Internal nrow function for ORFik experiment Number of runs in experiment", "topics": [ "nrow,experiment-method" ] }, { "page": "numExonsPerGroup", "title": "Get list of the number of exons per group", "topics": [ "numExonsPerGroup" ] }, { "page": "ofst_merge", "title": "Merge multiple ofst file", "topics": [ "ofst_merge" ] }, { "page": "optimizedTranscriptLengths", "title": "Load length and names of all transcripts", "topics": [ "optimizedTranscriptLengths" ] }, { "page": "optimizeTranscriptRegions", "title": "Make optimized GRangesList objects saved to disc", "topics": [ "optimizeTranscriptRegions" ] }, { "page": "orfFrameDistributions", "title": "Find shifted Ribo-seq frame distributions", "topics": [ "orfFrameDistributions" ] }, { "page": "ORFik.template.experiment", "title": "An ORFik experiment to see how it looks", "concept": [ "ORFik_experiment" ], "topics": [ "ORFik.template.experiment" ] }, { "page": "ORFik.template.experiment.zf", "title": "An ORFik experiment to see how it looks", "concept": [ "ORFik_experiment" ], "topics": [ "ORFik.template.experiment.zf" ] }, { "page": "ORFikQC", "title": "A post Alignment quality control of reads", "topics": [ "ORFikQC" ] }, { "page": "orfScore", "title": "Get ORFscore for a GRangesList of ORFs", "concept": [ "features" ], "topics": [ "orfScore" ] }, { "page": "organism-experiment-method", "title": "Get ORFik experiment organism", "concept": [ "ORFik_experiment" ], "topics": [ "organism,experiment-method" ] }, { "page": "outputLibs", "title": "Output NGS libraries to R as variables", "concept": [ "ORFik_experiment" ], "topics": [ "outputLibs" ] }, { "page": "pcaExperiment", "title": "Simple PCA analysis from ORFik experiment", "topics": [ "pcaExperiment" ] }, { "page": "pcaPlot", "title": "Simple PCA analysis from table", "topics": [ "pcaPlot" ] }, { "page": "pmapFromTranscriptF", "title": "Faster pmapFromTranscript", "topics": [ "pmapFromTranscriptF" ] }, { "page": "pmapToTranscriptF", "title": "Faster pmapToTranscript", "topics": [ "pmapToTranscriptF" ] }, { "page": "pseudoIntronsPerGroup", "title": "Get pseudo introns per Group", "topics": [ "pseudoIntronsPerGroup" ] }, { "page": "pSitePlot", "title": "Plot area around TIS as histogram", "concept": [ "coveragePlot" ], "topics": [ "pSitePlot" ] }, { "page": "QCfolder", "title": "Get path to ORFik experiment QC folder", "topics": [ "QCfolder" ] }, { "page": "QCfolder-experiment-method", "title": "Get path to ORFik experiment QC folder", "topics": [ "QCfolder,experiment-method" ] }, { "page": "QCreport", "title": "A post Alignment quality control of reads", "concept": [ "QC report" ], "topics": [ "QCreport" ] }, { "page": "QCstats", "title": "Load ORFik QC Statistics report", "concept": [ "QC report" ], "topics": [ "QCstats" ] }, { "page": "QCstats.plot", "title": "Make plot of ORFik QCreport", "topics": [ "QCstats.plot" ] }, { "page": "r", "title": "strandMode covRle", "topics": [ "r" ] }, { "page": "r-covRle-method", "title": "strandMode covRle", "topics": [ "r,covRle-method" ] }, { "page": "rankOrder", "title": "ORF rank in transcripts", "concept": [ "features" ], "topics": [ "rankOrder" ] }, { "page": "read_RDSQS", "title": "Read RDS or QS format file", "topics": [ "read_RDSQS" ] }, { "page": "read.experiment", "title": "Read ORFik 'experiment'", "concept": [ "ORFik_experiment" ], "topics": [ "read.experiment" ] }, { "page": "readBam", "title": "Custom bam reader", "concept": [ "utils" ], "topics": [ "readBam" ] }, { "page": "readBamIsUniqueMapper", "title": "Read unique mapper status from bam", "topics": [ "readBamIsUniqueMapper" ] }, { "page": "readBamSeqs", "title": "Read sequences from bam", "topics": [ "readBamSeqs" ] }, { "page": "readBigWig", "title": "Custom bigWig reader", "concept": [ "utils" ], "topics": [ "readBigWig" ] }, { "page": "readWidths", "title": "Get read widths", "topics": [ "readWidths" ] }, { "page": "readWig", "title": "Custom wig reader", "concept": [ "utils" ], "topics": [ "readWig" ] }, { "page": "reassignTSSbyCage", "title": "Reassign all Transcript Start Sites (TSS)", "concept": [ "CAGE" ], "topics": [ "reassignTSSbyCage" ] }, { "page": "reassignTxDbByCage", "title": "Input a txdb and reassign the TSS for each transcript by CAGE", "concept": [ "CAGE" ], "topics": [ "reassignTxDbByCage" ] }, { "page": "reduceKeepAttr", "title": "Reduce GRanges / GRangesList", "concept": [ "ExtendGenomicRanges" ], "topics": [ "reduceKeepAttr" ] }, { "page": "refFolder", "title": "Get path to ORFik experiment genome reference folder", "topics": [ "refFolder" ] }, { "page": "refFolder-experiment-method", "title": "Get path to ORFik experiment genome reference folder", "topics": [ "refFolder,experiment-method" ] }, { "page": "regionPerReadLength", "title": "Find proportion of reads per position per read length in region", "concept": [ "coverage" ], "topics": [ "regionPerReadLength" ] }, { "page": "remove.experiments", "title": "Remove ORFik experiment libraries load in R", "topics": [ "remove.experiments" ] }, { "page": "resFolder", "title": "Get ORFik experiment main output directory", "topics": [ "resFolder" ] }, { "page": "resFolder-experiment-method", "title": "Get ORFik experiment main output directory", "topics": [ "resFolder,experiment-method" ] }, { "page": "ribo_fft", "title": "Get periodogram data per read length", "topics": [ "ribo_fft" ] }, { "page": "ribo_fft_plot", "title": "Get periodogram plot per read length", "topics": [ "ribo_fft_plot" ] }, { "page": "riboORFs", "title": "Load Predicted translons", "topics": [ "riboORFs" ] }, { "page": "riboORFsFolder", "title": "Define folder for prediction output", "topics": [ "riboORFsFolder" ] }, { "page": "RiboQC.plot", "title": "Quality control for pshifted Ribo-seq data", "topics": [ "RiboQC.plot" ] }, { "page": "ribosomeReleaseScore", "title": "Ribosome Release Score (RRS)", "concept": [ "features" ], "topics": [ "ribosomeReleaseScore" ] }, { "page": "ribosomeStallingScore", "title": "Ribosome Stalling Score (RSS)", "concept": [ "features" ], "topics": [ "ribosomeStallingScore" ] }, { "page": "rnaNormalize", "title": "Normalize a data.table of coverage by RNA seq per position", "topics": [ "rnaNormalize" ] }, { "page": "runIDs", "title": "Get SRR/DRR/ERR run ids from ORFik experiment", "topics": [ "runIDs" ] }, { "page": "runIDs-experiment-method", "title": "Get SRR/DRR/ERR run ids from ORFik experiment", "topics": [ "runIDs,experiment-method" ] }, { "page": "save_RDSQS", "title": "Read RDS or QS format file", "topics": [ "save_RDSQS" ] }, { "page": "save.experiment", "title": "Save 'experiment' to disc", "concept": [ "ORFik_experiment" ], "topics": [ "save.experiment" ] }, { "page": "scaledWindowPositions", "title": "Scale (bin) windows to a meta window of given size", "concept": [ "coverage" ], "topics": [ "scaledWindowPositions" ] }, { "page": "scoreSummarizedExperiment", "title": "Helper function for makeSummarizedExperimentFromBam", "topics": [ "scoreSummarizedExperiment" ] }, { "page": "seqinfo-covRle-method", "title": "Seqinfo covRle Extracted from forward RleList", "topics": [ "seqinfo,covRle-method" ] }, { "page": "seqinfo-covRleList-method", "title": "Seqinfo covRle Extracted from forward RleList", "topics": [ "seqinfo,covRleList-method" ] }, { "page": "seqinfo-experiment-method", "title": "Seqinfo ORFik experiment Extracted from fasta genome index", "topics": [ "seqinfo,experiment-method" ] }, { "page": "seqlevels-covRle-method", "title": "Seqlevels covRle Extracted from forward RleList", "topics": [ "seqlevels,covRle-method" ] }, { "page": "seqlevels-covRleList-method", "title": "Seqlevels covRleList Extracted from forward RleList", "topics": [ "seqlevels,covRleList-method" ] }, { "page": "seqlevels-experiment-method", "title": "Seqlevels ORFik experiment Extracted from fasta genome index", "topics": [ "seqlevels,experiment-method" ] }, { "page": "seqnames-experiment-method", "title": "Seqnames ORFik experiment Extracted from fasta genome index", "topics": [ "seqnames,experiment-method" ] }, { "page": "seqnamesPerGroup", "title": "Get first seqname per GRangesList group", "topics": [ "seqnamesPerGroup" ] }, { "page": "shiftFootprints", "title": "Shift footprints by selected offsets", "concept": [ "pshifting" ], "topics": [ "shiftFootprints" ] }, { "page": "shiftFootprintsByExperiment", "title": "Shift footprints of each file in experiment", "concept": [ "pshifting" ], "topics": [ "shiftFootprintsByExperiment" ] }, { "page": "shiftPlots", "title": "Plot shifted heatmaps per library", "concept": [ "pshifting" ], "topics": [ "shiftPlots" ] }, { "page": "shifts_load", "title": "Load the shifts from experiment", "concept": [ "pshifting" ], "topics": [ "shifts_load" ] }, { "page": "shifts_save", "title": "Save shifts for Ribo-seq", "concept": [ "pshifting" ], "topics": [ "shifts_save" ] }, { "page": "show-covRle-method", "title": "covRle show definition", "topics": [ "show,covRle-method" ] }, { "page": "show-covRleList-method", "title": "covRleList show definition", "topics": [ "show,covRleList-method" ] }, { "page": "show-experiment-method", "title": "experiment show definition", "topics": [ "show,experiment-method" ] }, { "page": "simpleLibs", "title": "Converted format of NGS libraries", "topics": [ "simpleLibs" ] }, { "page": "sortPerGroup", "title": "Sort a GRangesList", "topics": [ "sortPerGroup" ] }, { "page": "STAR.align.folder", "title": "Align all libraries in folder with STAR", "concept": [ "STAR" ], "topics": [ "STAR.align.folder" ] }, { "page": "STAR.align.single", "title": "Align single or paired end pair with STAR", "concept": [ "STAR" ], "topics": [ "STAR.align.single" ] }, { "page": "STAR.allsteps.multiQC", "title": "Create STAR multiQC plot and table", "concept": [ "STAR" ], "topics": [ "STAR.allsteps.multiQC" ] }, { "page": "STAR.index", "title": "Create STAR genome index", "concept": [ "STAR" ], "topics": [ "STAR.index" ] }, { "page": "STAR.install", "title": "Download and prepare STAR", "concept": [ "STAR" ], "topics": [ "STAR.install" ] }, { "page": "STAR.multiQC", "title": "Create STAR multiQC plot and table", "concept": [ "STAR" ], "topics": [ "STAR.multiQC" ] }, { "page": "STAR.remove.crashed.genome", "title": "Remove crashed STAR genome", "concept": [ "STAR" ], "topics": [ "STAR.remove.crashed.genome" ] }, { "page": "start-GRanges-method", "title": "Get starts of GRanges", "topics": [ "start,GRanges-method" ] }, { "page": "startCodons", "title": "Get the Start codons(3 bases) from a GRangesList of orfs grouped by orfs", "concept": [ "ORFHelpers" ], "topics": [ "startCodons" ] }, { "page": "startDefinition", "title": "Returns start codon definitions", "concept": [ "findORFs" ], "topics": [ "startDefinition" ] }, { "page": "startRegion", "title": "Start region as GRangesList", "concept": [ "features" ], "topics": [ "startRegion" ] }, { "page": "startRegionCoverage", "title": "Start region coverage", "concept": [ "features" ], "topics": [ "startRegionCoverage" ] }, { "page": "startRegionString", "title": "Get start region as DNA-strings per GRanges group", "topics": [ "startRegionString" ] }, { "page": "startSites", "title": "Get the start sites from a GRangesList of orfs grouped by orfs", "concept": [ "ORFHelpers" ], "topics": [ "startSites" ] }, { "page": "stopCodons", "title": "Get the Stop codons (3 bases) from a GRangesList of orfs grouped by orfs", "concept": [ "ORFHelpers" ], "topics": [ "stopCodons" ] }, { "page": "stopDefinition", "title": "Returns stop codon definitions", "concept": [ "findORFs" ], "topics": [ "stopDefinition" ] }, { "page": "stopRegion", "title": "Stop region as GRangesList", "concept": [ "features" ], "topics": [ "stopRegion" ] }, { "page": "stopSites", "title": "Get the stop sites from a GRangesList of orfs grouped by orfs", "concept": [ "ORFHelpers" ], "topics": [ "stopSites" ] }, { "page": "strandBool", "title": "Get logical list of strands", "topics": [ "strandBool" ] }, { "page": "strandMode-covRle-method", "title": "strandMode covRle", "topics": [ "strandMode,covRle-method" ] }, { "page": "strandMode-covRleList-method", "title": "strandMode covRle", "topics": [ "strandMode,covRleList-method" ] }, { "page": "strandPerGroup", "title": "Get first strand per GRangesList group", "topics": [ "strandPerGroup" ] }, { "page": "subsetToFrame", "title": "Subset GRanges to get desired frame.", "topics": [ "subsetToFrame" ] }, { "page": "sum-covRle-method", "title": "sum covRle", "topics": [ "sum,covRle-method" ] }, { "page": "symbols", "title": "Get ORFik experiment gene symbols", "topics": [ "symbols" ] }, { "page": "symbols-experiment-method", "title": "Get path to ORFik experiment QC folder", "topics": [ "symbols,experiment-method" ] }, { "page": "te_rna.plot", "title": "Translational efficiency plots", "concept": [ "DifferentialExpression" ], "topics": [ "te_rna.plot" ] }, { "page": "te.plot", "title": "Translational efficiency plots", "topics": [ "te.plot" ] }, { "page": "te.table", "title": "Create a TE table", "concept": [ "DifferentialExpression" ], "topics": [ "te.table" ] }, { "page": "template_shift_table", "title": "Make template for shift table of experiment", "topics": [ "template_shift_table" ] }, { "page": "tile1", "title": "Tile each GRangesList group to 1-base resolution.", "concept": [ "ExtendGenomicRanges" ], "topics": [ "tile1" ] }, { "page": "TOP.Motif.ecdf", "title": "TOP Motif ecdf plot", "topics": [ "TOP.Motif.ecdf" ] }, { "page": "topMotif", "title": "TOP Motif detection", "topics": [ "topMotif" ] }, { "page": "transcriptWindow", "title": "Make 100 bases size meta window for all libraries in experiment", "concept": [ "experiment plots" ], "topics": [ "transcriptWindow" ] }, { "page": "translationalEff", "title": "Translational efficiency", "concept": [ "features" ], "topics": [ "translationalEff" ] }, { "page": "trimming.table", "title": "Create trimming table", "topics": [ "trimming.table" ] }, { "page": "txNames", "title": "Get transcript names from orf names", "concept": [ "ORFHelpers" ], "topics": [ "txNames" ] }, { "page": "txNamesToGeneNames", "title": "Convert transcript names to gene names", "topics": [ "txNamesToGeneNames" ] }, { "page": "txSeqsFromFa", "title": "Get transcript sequence from a GRangesList and a faFile or BSgenome", "concept": [ "ExtendGenomicRanges" ], "topics": [ "txSeqsFromFa" ] }, { "page": "uniqueGroups", "title": "Get the unique set of groups in a GRangesList", "concept": [ "ORFHelpers" ], "topics": [ "uniqueGroups" ] }, { "page": "uniqueMappers", "title": "Get ORFik uniqueMappers status", "topics": [ "uniqueMappers" ] }, { "page": "uniqueMappers-experiment-method", "title": "Get ORFik uniqueMappers status", "topics": [ "uniqueMappers,experiment-method" ] }, { "page": "uniqueMappers-NULL-method", "title": "Get ORFik uniqueMappers status", "topics": [ "uniqueMappers,NULL-method" ] }, { "page": "uniqueMappers-set", "title": "Set ORFik uniqueMappers status", "topics": [ "uniqueMappers<-" ] }, { "page": "uniqueMappers-set-experiment-method", "title": "Set ORFik uniqueMappers status", "topics": [ "uniqueMappers<-,experiment-method" ] }, { "page": "uniqueOrder", "title": "Get unique ordering for GRangesList groups", "concept": [ "ORFHelpers" ], "topics": [ "uniqueOrder" ] }, { "page": "unlistGrl", "title": "Safe unlist", "topics": [ "unlistGrl" ] }, { "page": "unlistToExtremities", "title": "Get flanks as GRanges", "topics": [ "unlistToExtremities" ] }, { "page": "uORFSearchSpace", "title": "Create search space to look for uORFs", "concept": [ "uorfs" ], "topics": [ "uORFSearchSpace" ] }, { "page": "width-GRanges-method", "title": "Get widths of GRanges", "topics": [ "width,GRanges-method" ] }, { "page": "widthPerGroup", "title": "Get total widths per GRangesList group", "topics": [ "widthPerGroup" ] }, { "page": "windowCoveragePlot", "title": "Get meta coverage plot of reads", "concept": [ "coveragePlot" ], "topics": [ "windowCoveragePlot" ] }, { "page": "windowPerGroup", "title": "Get window region of GRanges object", "concept": [ "ExtendGenomicRanges" ], "topics": [ "windowPerGroup" ] }, { "page": "windowPerReadLength", "title": "Find proportion of reads per position per read length in window", "concept": [ "coverage" ], "topics": [ "windowPerReadLength" ] } ], "_readme": "https://github.com/bioc/ORFik/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocParallel", "biomaRt", "biomartr", "Biostrings", "bit", "bit64", "bitops", "blob", "BSgenome", "cachem", "cigarillo", "cli", "clipr", "codetools", "cowplot", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "DESeq2", "digest", "downloader", "dplyr", "farver", "fastmap", "filelock", "formatR", "fs", "fst", "fstcore", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "gridExtra", "gtable", "hms", "httr", "httr2", "IRanges", "isoband", "jsonlite", "KEGGREST", "KernSmooth", "labeling", "lambda.r", "lattice", "lifecycle", "locfit", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "philentropy", "pillar", "pkgconfig", "png", "poorman", "prettyunits", "progress", "purrr", "qs2", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "RColorBrewer", "Rcpp", 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and gtf file)", "Download genome and gtf files", "Contaminants", "Local annotation", "Annotation without defined UTRs", "Create 5' UTR annotation from CAGE", "Create Pseudo 5' UTR annotation", "Fixing malformed gtf/gff", "RNA-seq alignment", "Indexing", "Trimming and Aligning the data", "Trimming data", "Aligning the data", "UMIs", "Collapsing duplicated reads", "Solving errors when aligning:", "RAM usage warnings", "Systems that restricts max open files", "Restart STAR from crashed step", "Create an ORFik experiment of the Yeast data", "Post alignment QC report", "Convert libraries to new formats", "Outputting libraries to R", "FPKM values (normalized counts)" ], "created": "2022-10-27 15:44:24", "modified": "2025-05-06 07:07:41", "commits": 7 }, { "source": "ORFikExperiment.Rmd", "filename": "ORFikExperiment.html", "title": "Data management", "author": "Haakon Tjeldnes & Kornel Labun", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Motivation", "What is an ORFik experiment?", "creating an ORFik experiment", "A minimal experiment", "Fixing or updating an experiment", "ORFik example experiment", "The experiment object", "Accessing library file paths", "Loading data from experiment", "Loading NGS data to environment", "Loading NGS data as list", "Loading NGS data by fimport", "Loading Annotation and specific regions", "Plotting with ORFik experiments", "P-site shifting experiment", "Converting bam files to faster formats", "ofst: ORFik serialized format", "bedo: bed ORFik file (to be deprecated!)", "bedoc: bed ORFik file with cigar (to be deprecated!)", "ORFik QC report", "General report", "How to run QC:", "How to load optimized output from QC:", "How to load the QC statistics:", "How to see the QC plots:", "Ribo-seq specific pshifting and QC", "Using the ORFik experiment system in your script", "Note for windows users", "Looping over all libraries in experiment", "Reformat output to data.table (merge column-wise)", "Reformat output to data.table (merge row-wise)", "Conclusion" ], "created": "2022-10-27 15:44:24", "modified": "2024-12-13 11:59:09", "commits": 4 }, { "source": "Importing_Data.Rmd", "filename": "Importing_Data.html", "title": "Importing data", "author": "Haakon Tjeldnes & Kornel Labun", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Motivation", "Importing Sequencing reads", "Loading files (general)", "Bam files", "Other formats", "Exporting to new formats", "Files are not preload into R", "BAM to OFST (keep cigar information)", "BAM to bigwig (do not keep cigar information or read lengths)", "Files are preload into R", "Random access", "Importing Annotation", "Loading Genome index (fasta index)", "Loading Gene annotation (Txdb)", "Loading Transcript regions", "Loading Transcript regions (filtering)", "Loading Transcript regions (filtering by length requirements)", "Loading Transcript regions (filtering by canonical isoform)", "Loading uORF annotation" ], "created": "2023-03-23 13:58:56", "modified": "2024-10-02 17:27:56", "commits": 9 }, { "source": "ORFikOverview.Rmd", "filename": "ORFikOverview.html", "title": "ORFik Overview", "author": "Haakon Tjeldnes & Kornel Labun", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Finding Open Reading Frames", "Example of finding ORFs in on 5' UTR of hg19", "Saving coordinates of ORFs to disc", "Getting sequences from ORFs", "Getting DNA fasta sequences of ORFs", "Amino acid sequences of ORFs", "New GRanges and GRangesList utilities for ORFs", "Grouping ORFs", "Filtering example", "ORF interest regions", "When to use which ORF-finding function", "Finding ORFs in spliced transcripts", "Prokaryote/Circular Genomes and fasta transcriptomes.", "Filter on strand", "CAGE data for 5' UTR re-annotation", "RiboSeq footprints automatic shift detection and shifting", "Gene identity functions for ORFs or genes", "Calculating Kozak sequence score for ORFs", "Using ORFik in your package or scripts", "Coverage plots made easy with ORFik", "Multiple data sets in one plot", "Conclusion" ], "created": "2017-11-22 15:33:59", "modified": "2024-06-05 13:32:38", "commits": 67 }, { "source": "Ribo-seq_pipeline-human.Rmd", "filename": "Ribo-seq_pipeline-human.html", "title": "Ribo-seq pipeline (Yeast)", "author": "Haakon Tjeldnes & Kornel Labun", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Pipeline" ], "created": "2025-05-06 07:07:41", "modified": "2025-05-06 07:07:41", "commits": 1 }, { "source": "Ribo-seq_pipeline-yeast.Rmd", "filename": "Ribo-seq_pipeline-yeast.html", "title": "Ribo-seq pipeline (Yeast)", "author": "Haakon Tjeldnes & Kornel Labun", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Pipeline" ], "created": "2025-05-06 07:07:41", "modified": "2025-05-06 07:07:41", "commits": 1 }, { "source": "Working_with_transcripts.Rmd", "filename": "Working_with_transcripts.html", "title": "Working with transcripts", "author": "Haakon Tjeldnes & Kornel Labun", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Motivation", "Getting data", "Loading Transcript region (single point locations)", "Loading Transcript region (window locations)", "Extending transcript into genomic flanks", "Coverage over transcript regions", "Loading NGS data", "Total counts per region/window", "Per nucleotide in region/window", "Per nucleotide in region/window (split by read length)", "Advanced details" ], "created": "2023-03-23 13:58:56", "modified": "2023-08-04 20:45:20", "commits": 4 } ], "_score": 10.342376643167086, "_indexed": true, "_nocasepkg": "orfik", "_universes": [ "bioc", "roleren" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.33.0", "date": "2026-05-30T07:28:51.000Z", "distro": "noble", "arch": "aarch64", "commit": "bcf19ce8103042e4b1babe8e2399223f3dd45dc6", "fileid": "9bee1ed3eefd776af6903806b3b69e5477f813b20fd0ec2c20f5338c6076e2e1", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677837038" }, { "r": 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