Open Reading Frames in Genomics
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Documentation for package ‘ORFik’ version 1.29.7
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A B C D E F G H I K L M N O P Q R S T U W
| ORFik-package | ORFik for analysis of open reading frames. |
-- A --
| add_pseudo_5utrs_txdb_if_needed | add_pseudo_5utrs_txdb_if_needed |
| append_gene_symbols | Append gene symbols to a data.table with tx ids |
| artificial.orfs | Create small artificial orfs from cds |
| assignTSSByCage | Input a txdb and add a 5' leader for each transcript, that does not have one. |
| asTX | Map genomic to transcript coordinates by reference |
-- B --
| bamVarName | Get library variable names from ORFik 'experiment' |
| browseSRA | Open SRA in browser for specific bioproject |
-- C --
| canonical_isoforms | Get canonical isoforms of organism |
| canonical_isoforms-method | Get canonical isoforms of organism |
| codon_usage | Codon usage |
| codon_usage_exp | Codon analysis for ORFik experiment |
| codon_usage_plot | Plot codon_usage |
| collapse.fastq | Very fast fastq/fasta collapser |
| collapseDuplicatedReads | Collapse duplicated reads |
| collapseDuplicatedReads-method | Collapse duplicated reads |
| collapseDuplicatedReads-method | Collapse duplicated reads |
| collapseDuplicatedReads-method | Collapse duplicated reads |
| collapseDuplicatedReads-method | Collapse duplicated reads |
| combn.pairs | Create all unique combinations pairs possible |
| computeFeatures | Get all main features in ORFik |
| computeFeaturesCage | Get all main features in ORFik |
| config | Read directory config for ORFik experiments |
| config.exper | Set directories for experiment |
| config.save | Save/update directory config for ORFik experiments |
| config_file | Get path for ORFik config in cache |
| convertLibs | Converted format of NGS libraries |
| convertToOneBasedRanges | Convert a GRanges Object to 1 width reads |
| convert_bam_to_ofst | Convert libraries to ofst |
| convert_to_bigWig | Convert to BigWig |
| convert_to_covRle | Convert libraries to covRle |
| convert_to_covRleList | Convert libraries to covRleList objects |
| convert_to_fstWig | Convert to fstwig |
| correlation.plots | Correlation plots between all samples |
| cor_plot | Get correlation between columns |
| cor_table | Get correlation between columns |
| countOverlapsW | CountOverlaps with weights |
| countTable | Extract count table directly from experiment |
| countTable_regions | Make a list of count matrices from experiment |
| coverageByTranscriptC | coverageByTranscript with coverage input |
| coverageByTranscriptFST | Get coverage from fst large coverage format |
| coverageByTranscriptW | coverageByTranscript with weights |
| coverageHeatMap | Create a heatmap of coverage |
| coveragePerTiling | Get coverage per group |
| coverageScorings | Add a coverage scoring scheme |
| coverage_to_dt | Convert coverage RleList to data.table |
| covRle | Coverage Rlelist for both strands |
| covRle-class | Coverage Rle for both strands or single |
| covRleFromGR | Convert GRanges to covRle |
| covRleList | Coverage Rlelist for both strands |
| covRleList-class | List of covRle |
| create.experiment | Create an ORFik 'experiment' |
-- D --
| defineTrailer | Defines trailers for ORF. |
| DEG.analysis | Run differential TE analysis |
| DEG.plot.static | Plot DEG result |
| DEG_gorilla | GO analysis with GOrilla |
| DEG_model | Get DESeq2 model without running results |
| DEG_model_results | Get DESeq2 model results from DESeqDataSet |
| DEG_model_simple | Simple Fpkm ratio test DEG |
| design-method | 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. |
| detectRibosomeShifts | Detect ribosome shifts |
| detect_ribo_orfs | Detect ORFs by Ribosome profiling data |
| disengagementScore | Disengagement score (DS) |
| distanceToFollowing | Distance to following range group |
| distanceToPreceding | Distance to preceding range group |
| distToCds | Get distances between ORF ends and starts of their transcripts cds. |
| distToTSS | Get distances between ORF Start and TSS of its transcript |
| download.SRA | Download read libraries from SRA |
| download.SRA.metadata | Downloads metadata from SRA |
| download_gene_homologues | Download homologue information of a gene |
| download_gene_info | Download summary information of a gene |
| DTEG.analysis | Run differential TE analysis |
| DTEG.plot | Plot DTEG result |
-- E --
| entropy | Percentage of maximum entropy |
| envExp | Get ORFik experiment environment |
| envExp-method | Get ORFik experiment environment |
| envExp<- | Set ORFik experiment environment |
| envExp<--method | Set ORFik experiment environment |
| exonsWithPseudoIntronsPerGroup | Get exons with pseudo introns per Group |
| experiment | experiment class definition |
| experiment-class | experiment class definition |
| experiment.colors | Decide color for libraries by grouping |
| export.bed12 | Export as bed12 format |
| export.bedo | Store GRanges object as .bedo |
| export.bedoc | Store GAlignments object as .bedoc |
| export.bigWig | Export as bigWig format |
| export.fstwig | Export as fstwig (fastwig) format |
| export.ofst | Store GRanges / GAlignments object as .ofst |
| export.ofst-method | Store GRanges / GAlignments object as .ofst |
| export.ofst-method | Store GRanges / GAlignments object as .ofst |
| export.ofst-method | Store GRanges / GAlignments object as .ofst |
| export.wiggle | Export as wiggle format |
| extendLeaders | Extend the leaders transcription start sites. |
| extendLeadersUntil | Extend Leaders Until |
| extendTrailers | Extend the Trailers transcription stop sites |
| extendTrailersUntil | Extend Trailers Until |
| extract_run_id | Extract SRR/ERR/DRR run IDs from string |
-- F --
| f | strandMode covRle |
| f-method | strandMode covRle |
| filepath | Get filepaths to ORFik experiment |
| file_ext_without_compression | Get file extension of files without compressions |
| filterExtremePeakGenes | Filter out transcript by a median filter |
| filterTranscripts | Filter transcripts by lengths |
| fimport | Load any type of sequencing reads |
| findFa | Convenience wrapper for Rsamtools FaFile |
| findMapORFs | Find ORFs and immediately map them to their genomic positions. |
| findORFs | Find Open Reading Frames. |
| findORFsFasta | Finds Open Reading Frames in fasta files. |
| findPeaksPerGene | Find peaks per gene |
| findUORFs | Find upstream ORFs from transcript annotation |
| findUORFs_exp | Find upstream ORFs from transcript annotation |
| find_url_ebi | Locates and check if fastq files exists in ebi |
| firstEndPerGroup | Get first end per granges group |
| firstExonPerGroup | Get first exon per GRangesList group |
| firstStartPerGroup | Get first start per granges group |
| fix_malformed_gff | Fix a malformed gff file |
| flankPerGroup | Get flanks per group |
| floss | Fragment Length Organization Similarity Score |
| fpkm | Create normalizations of overlapping read counts. |
| fractionLength | Fraction Length |
| fread.bed | Load bed file as GRanges |
-- G --
| gcContent | Get GC content |
| geneToSymbol | Get gene symbols from Ensembl gene ids |
| getGenomeAndAnnotation | Download genome (fasta), annotation (GTF) and contaminants |
| get_bioproject_candidates | Query eutils for bioproject IDs |
| get_silva_rRNA | Download Silva SSU & LSU sequences |
| get_system_usage | System usage for Linux (Auto-detects correct drive if not provided) |
| go_analaysis_gorilla | GO analysis with GOrilla |
| groupGRangesBy | Group GRanges |
| groupings | Get number of ranges per group as an iteration |
-- H --
| heatMapRegion | Create coverage heatmaps of specified region |
| heatMap_single | Coverage heatmap of single libraries |
-- I --
| import.bedo | Load GRanges object from .bedo |
| import.bedoc | Load GAlignments object from .bedoc |
| import.fstwig | Import region from fastwig |
| import.ofst | Load GRanges / GAlignments object from .ofst |
| importGtfFromTxdb | Import the GTF / GFF that made the txdb |
| initiationScore | Get initiation score for a GRangesList of ORFs |
| insideOutsideORF | Inside/Outside score (IO) |
| install.fastp | Download and prepare fastp trimmer |
| install.sratoolkit | Download sra toolkit |
| isInFrame | Find frame for each orf relative to cds |
| isOverlapping | Find frame for each orf relative to cds |
-- K --
| kozakHeatmap | Make sequence region heatmap relative to scoring |
| kozakSequenceScore | Make a score for each ORFs start region by proximity to Kozak |
| kozak_IR_ranking | Rank kozak initiation sequences |
-- L --
| lastExonEndPerGroup | Get last end per granges group |
| lastExonPerGroup | Get last exon per GRangesList group |
| lastExonStartPerGroup | Get last start per granges group |
| length-method | length covRle |
| length-method | length covRleList |
| lengths-method | lengths covRle |
| lengths-method | lengths covRleList |
| libFolder | Get path to ORFik experiment library folder |
| libFolder-method | Get path to ORFik experiment library folder |
| libraryTypes | Which type of library type in 'experiment'? |
| list.experiments | List current experiment available |
| list.genomes | List genomes created with ORFik |
| loadRegion | Load transcript region |
| loadRegions | Get all regions of transcripts specified to environment |
| loadTranscriptType | Load transcripts of given biotype |
| loadTxdb | General loader for txdb |
| longestORFs | Get longest ORF per stop site |
-- M --
| makeORFNames | Make ORF names per orf |
| makeSummarizedExperimentFromBam | Make a count matrix from a library or experiment |
| makeSymbols | Make Gene symbols from txdb |
| makeTxdbFromGenome | Make txdb from genome |
| mergeFastq | Merge groups of Fastq /Fasta files |
| mergeLibs | Merge and save libraries of experiment |
| metadata.autnaming | Guess SRA metadata columns |
| metaWindow | Calculate meta-coverage of reads around input GRanges/List object. |
| model.matrix-method | Get experiment design model matrix |
-- N --
| name | Get name of ORFik experiment |
| name-method | Get name of ORFik experiment |
| nrow-method | Internal nrow function for ORFik experiment Number of runs in experiment |
| numExonsPerGroup | Get list of the number of exons per group |
-- O --
| ofst_merge | Merge multiple ofst file |
| optimizedTranscriptLengths | Load length and names of all transcripts |
| optimizeTranscriptRegions | Make optimized GRangesList objects saved to disc |
| orfFrameDistributions | Find shifted Ribo-seq frame distributions |
| ORFik | ORFik for analysis of open reading frames. |
| ORFik.template.experiment | An ORFik experiment to see how it looks |
| ORFik.template.experiment.zf | An ORFik experiment to see how it looks |
| ORFikQC | A post Alignment quality control of reads |
| orfScore | Get ORFscore for a GRangesList of ORFs |
| organism-method | Get ORFik experiment organism |
| outputLibs | Output NGS libraries to R as variables |
-- P --
| pcaExperiment | Simple PCA analysis from ORFik experiment |
| pcaPlot | Simple PCA analysis from table |
| pmapFromTranscriptF | Faster pmapFromTranscript |
| pmapToTranscriptF | Faster pmapToTranscript |
| pseudoIntronsPerGroup | Get pseudo introns per Group |
| pSitePlot | Plot area around TIS as histogram |
-- Q --
| QCfolder | Get path to ORFik experiment QC folder |
| QCfolder-method | Get path to ORFik experiment QC folder |
| QCreport | A post Alignment quality control of reads |
| QCstats | Load ORFik QC Statistics report |
| QCstats.plot | Make plot of ORFik QCreport |
-- R --
| r | strandMode covRle |
| r-method | strandMode covRle |
| rankOrder | ORF rank in transcripts |
| read.experiment | Read ORFik 'experiment' |
| readBam | Custom bam reader |
| readBigWig | Custom bigWig reader |
| readWidths | Get read widths |
| readWig | Custom wig reader |
| read_RDSQS | Read RDS or QS format file |
| reassignTSSbyCage | Reassign all Transcript Start Sites (TSS) |
| reassignTxDbByCage | Input a txdb and reassign the TSS for each transcript by CAGE |
| reduceKeepAttr | Reduce GRanges / GRangesList |
| refFolder | Get path to ORFik experiment genome reference folder |
| refFolder-method | Get path to ORFik experiment genome reference folder |
| regionPerReadLength | Find proportion of reads per position per read length in region |
| remove.experiments | Remove ORFik experiment libraries load in R |
| resFolder | Get ORFik experiment main output directory |
| resFolder-method | Get ORFik experiment main output directory |
| riboORFs | Load Predicted translons |
| riboORFsFolder | Define folder for prediction output |
| RiboQC.plot | Quality control for pshifted Ribo-seq data |
| ribosomeReleaseScore | Ribosome Release Score (RRS) |
| ribosomeStallingScore | Ribosome Stalling Score (RSS) |
| ribo_fft | Get periodogram data per read length |
| ribo_fft_plot | Get periodogram plot per read length |
| rnaNormalize | Normalize a data.table of coverage by RNA seq per position |
| runIDs | Get SRR/DRR/ERR run ids from ORFik experiment |
| runIDs-method | Get SRR/DRR/ERR run ids from ORFik experiment |
-- S --
| save.experiment | Save 'experiment' to disc |
| save_RDSQS | Read RDS or QS format file |
| scaledWindowPositions | Scale (bin) windows to a meta window of given size |
| scoreSummarizedExperiment | Helper function for makeSummarizedExperimentFromBam |
| seqinfo-method | Seqinfo covRle Extracted from forward RleList |
| seqinfo-method | Seqinfo covRle Extracted from forward RleList |
| seqinfo-method | Seqinfo ORFik experiment Extracted from fasta genome index |
| seqlevels-method | Seqlevels covRle Extracted from forward RleList |
| seqlevels-method | Seqlevels covRleList Extracted from forward RleList |
| seqlevels-method | Seqlevels ORFik experiment Extracted from fasta genome index |
| seqnames-method | Seqnames ORFik experiment Extracted from fasta genome index |
| seqnamesPerGroup | Get list of seqnames per granges group |
| shiftFootprints | Shift footprints by selected offsets |
| shiftFootprintsByExperiment | Shift footprints of each file in experiment |
| shiftPlots | Plot shifted heatmaps per library |
| shifts_load | Load the shifts from experiment |
| shifts_save | Save shifts for Ribo-seq |
| show-method | covRle show definition |
| show-method | covRleList show definition |
| show-method | experiment show definition |
| simpleLibs | Converted format of NGS libraries |
| sortPerGroup | Sort a GRangesList |
| STAR.align.folder | Align all libraries in folder with STAR |
| STAR.align.single | Align single or paired end pair with STAR |
| STAR.allsteps.multiQC | Create STAR multiQC plot and table |
| STAR.index | Create STAR genome index |
| STAR.install | Download and prepare STAR |
| STAR.multiQC | Create STAR multiQC plot and table |
| STAR.remove.crashed.genome | Remove crashed STAR genome |
| startCodons | Get the Start codons(3 bases) from a GRangesList of orfs grouped by orfs |
| startDefinition | Returns start codon definitions |
| startRegion | Start region as GRangesList |
| startRegionCoverage | Start region coverage |
| startRegionString | Get start region as DNA-strings per GRanges group |
| startSites | Get the start sites from a GRangesList of orfs grouped by orfs |
| stopCodons | Get the Stop codons (3 bases) from a GRangesList of orfs grouped by orfs |
| stopDefinition | Returns stop codon definitions |
| stopRegion | Stop region as GRangesList |
| stopSites | Get the stop sites from a GRangesList of orfs grouped by orfs |
| strandBool | Get logical list of strands |
| strandMode-method | strandMode covRle |
| strandMode-method | strandMode covRle |
| strandPerGroup | Get list of strands per granges group |
| subsetToFrame | Subset GRanges to get desired frame. |
| sum-method | sum covRle |
| symbols | Get ORFik experiment gene symbols |
| symbols-method | Get path to ORFik experiment QC folder |
-- T --
| te.plot | Translational efficiency plots |
| te.table | Create a TE table |
| te_rna.plot | Translational efficiency plots |
| tile1 | Tile each GRangesList group to 1-base resolution. |
| TOP.Motif.ecdf | TOP Motif ecdf plot |
| topMotif | TOP Motif detection |
| transcriptWindow | Make 100 bases size meta window for all libraries in experiment |
| translationalEff | Translational efficiency |
| trimming.table | Create trimming table |
| txNames | Get transcript names from orf names |
| txNamesToGeneNames | Convert transcript names to gene names |
| txSeqsFromFa | Get transcript sequence from a GRangesList and a faFile or BSgenome |
-- U --
| uniqueGroups | Get the unique set of groups in a GRangesList |
| uniqueOrder | Get unique ordering for GRangesList groups |
| unlistGrl | Safe unlist |
| unlistToExtremities | Get flanks as GRanges |
| uORFSearchSpace | Create search space to look for uORFs |
-- W --
| widthPerGroup | Get list of widths per granges group |
| windowCoveragePlot | Get meta coverage plot of reads |
| windowPerGroup | Get window region of GRanges object |
| windowPerReadLength | Find proportion of reads per position per read length in window |