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