| addCdsOnLeaderEnds | Extends leaders downstream |
| addNewTSSOnLeaders | Add cage max peaks as new transcript start sites for each 5'... |
| add_pseudo_5utrs_txdb_if_needed | add_pseudo_5utrs_txdb_if_needed |
| alignmentFeatureStatistics | Create alignment feature statistcs |
| allFeaturesHelper | Calculate the features in computeFeatures function |
| appendZeroes | Append zero values to data.table |
| artificial.orfs | Create small artificial orfs from cds |
| assignAnnotations | Overlaps GRanges object with provided annotations. |
| assignFirstExonsStartSite | Reassign the start positions of the first exons per group in... |
| assignLastExonsStopSite | Reassign the stop positions of the last exons per group |
| assignTSSByCage | Input a txdb and add a 5' leader for each transcript, that... |
| asTX | Map genomic to transcript coordinates by reference |
| bamVarName | Get library variable names from ORFik 'experiment' |
| bamVarNamePicker | Get variable name per filepath in experiment |
| batchNames | Get batch name variants |
| bedToGR | Converts bed style data.frame to GRanges |
| browseSRA | Open SRA in browser for specific bioproject |
| cellLineNames | Get cell-line name variants |
| cellTypeNames | Get cell type name variants |
| changePointAnalysis | Get the offset for specific RiboSeq read width |
| checkRFP | Helper Function to check valid RFP input |
| checkRNA | Helper Function to check valid RNA input |
| codonSumsPerGroup | Get read hits per codon |
| codon_usage | Codon usage |
| codon_usage_exp | Codon analysis for ORFik experiment |
| codon_usage_plot | Plot codon_usage |
| collapse.by.scores | Merge reads by sum of existing scores |
| 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 | Collapse duplicated reads |
| collapse.fastq | Very fast fastq/fasta collapser |
| combn.pairs | Create all unique combinations pairs possible |
| computeFeatures | Get all main features in ORFik |
| computeFeaturesCage | Get all main features in ORFik |
| conditionNames | Get condition name variants |
| config | Read directory config for ORFik experiments |
| config.exper | Set directories for experiment |
| config_file | Get path for ORFik config in cache |
| config.save | Save/update directory config for ORFik experiments |
| convert_bam_to_ofst | Convert libraries to ofst |
| convertLibs | Converted format of NGS libraries |
| 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 |
| convertToOneBasedRanges | Convert a GRanges Object to 1 width reads |
| cor_plot | Get correlation between columns |
| correlation.plots | Correlation plots between all samples |
| 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 |
| coverageByTranscriptW | coverageByTranscript with weights |
| coverageGroupings | Get grouping for a coverage table in ORFik |
| 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' |
| defineIsoform | Overlaps GRanges object with provided annotations. |
| defineTrailer | Defines trailers for ORF. |
| DEG.analysis | Run differential TE analysis |
| 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 |
| DEG.plot.static | Plot DEG result |
| design-experiment-method | Get experimental design Find the column/columns that create a... |
| detect_ribo_orfs | Detect ORFs by Ribosome profiling data |
| detectRibosomeShifts | Detect ribosome shifts |
| 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... |
| distToTSS | Get distances between ORF Start and TSS of its transcript |
| download.ebi | Faster download of fastq files |
| download.SRA | Download read libraries from SRA |
| download.SRA.metadata | Downloads metadata from SRA |
| downstreamFromPerGroup | Get rest of objects downstream (inclusive) |
| downstreamN | Restrict GRangesList |
| downstreamOfPerGroup | Get rest of objects downstream (exclusive) |
| DTEG.analysis | Run differential TE analysis |
| DTEG.plot | Plot DTEG result |
| entropy | Percentage of maximum entropy |
| envExp | Get ORFik experiment environment |
| envExp-experiment-method | Get ORFik experiment environment |
| envExp-set | Set ORFik experiment environment |
| envExp-set-experiment-method | Set ORFik experiment environment |
| exists.ftp.dir.fast | A fast ftp directory check |
| exists.ftp.file.fast | A fast ftp file check |
| 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-GAlignmentPairs-method | Store GRanges / GAlignments object as .ofst |
| export.ofst-GAlignments-method | Store GRanges / GAlignments object as .ofst |
| export.ofst-GRanges-method | Store GRanges / GAlignments object as .ofst |
| export.wiggle | Export as wiggle format |
| extendLeaders | Extend the leaders transcription start sites. |
| extendLeadersUntil | Extend Leaders Until |
| extendsTSSexons | Extend first exon of each transcript with length specified |
| extendTrailers | Extend the Trailers transcription stop sites |
| extendTrailersUntil | Extend Trailers Until |
| extract_run_id | Extract SRR/ERR/DRR run IDs from string |
| f | strandMode covRle |
| f-covRle-method | strandMode covRle |
| file_ext_without_compression | Get file extension of files without compressions |
| filepath | Get filepaths to ORFik experiment |
| filterCage | Filter peak of cage-data by value |
| filterExtremePeakGenes | Filter out transcript by a median filter |
| filterTranscripts | Filter transcripts by lengths |
| filterUORFs | Remove uORFs that are false CDS hits |
| fimport | Load any type of sequencing reads |
| findFa | Convenience wrapper for Rsamtools FaFile |
| findFromPath | Find all candidate library types filenames |
| findLibrariesInFolder | Get all library files in folder/folders of given types |
| findMapORFs | Find ORFs and immediately map them to their genomic... |
| findMaxPeaks | Find max peak for each transcript, returns as data.table,... |
| findNewTSS | Finds max peaks per trancsript from reads in the cagefile |
| findNGSPairs | Find pair of forward and reverse strand wig / bed files and... |
| 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 |
| find_url_ebi_safe | Find URL for EBI fastq files |
| 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 |
| footprints.analysis | Pre shifting plot analysis |
| fpkm | Create normalizations of overlapping read counts. |
| fpkm_calc | Create normalizations of read counts |
| fractionLength | Fraction Length |
| fractionNames | Get cell fraction name variants |
| fread.bed | Load bed file as GRanges |
| gcContent | Get GC content |
| geneToSymbol | Get gene symbols from Ensembl gene ids |
| get_bioproject_candidates | Query eutils for bioproject IDs |
| getGAlignments | Internal GAlignments loader from fst data.frame |
| getGAlignmentsPairs | Internal GAlignmentPairs loader from fst data.frame |
| getGenomeAndAnnotation | Download genome (fasta), annotation (GTF) and contaminants |
| get_genome_fasta | Download genome (fasta), annotation (GTF) and contaminants |
| get_genome_gtf | Download genome (fasta), annotation (GTF) and contaminants |
| getGRanges | Internal GRanges loader from fst data.frame |
| getGtfPathFromTxdb | Get path of GTF that created txdb |
| getNGenesCoverage | Get number of genes per coverage table |
| get_noncoding_rna | Download genome (fasta), annotation (GTF) and contaminants |
| get_phix_genome | Download genome (fasta), annotation (GTF) and contaminants |
| get_silva_rRNA | Download Silva SSU & LSU sequences |
| getWeights | Get weights from a subject GenomicRanges object |
| groupGRangesBy | Group GRanges |
| groupings | Get number of ranges per group as an iteration |
| gSort | Sort a GRangesList, helper. |
| hasHits | Hits from reads |
| heatMapL | Coverage heatmap of multiple libraries |
| heatMapRegion | Create coverage heatmaps of specified region |
| heatMap_single | Coverage heatmap of single libraries |
| import.bedo | Load GRanges object from .bedo |
| import.bedoc | Load GAlignments object from .bedoc |
| import.fstwig | Import region from fastwig |
| importGtfFromTxdb | Import the GTF / GFF that made the txdb |
| import.ofst | Load GRanges / GAlignments object from .ofst |
| inhibitorNames | Get translocation inhibitor name variants |
| 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 |
| is.grl | Helper function to check for GRangesList |
| is.gr_or_grl | Helper function to check for GRangesList or GRanges class |
| isInFrame | Find frame for each orf relative to cds |
| is.ORF | Check if all requirements for an ORFik ORF is accepted. |
| isOverlapping | Find frame for each orf relative to cds |
| isPeriodic | Find if there is a periodicity of 3 in the vector |
| is.range | Helper function to check for ranged object |
| kozakHeatmap | Make sequence region heatmap relative to scoring |
| kozak_IR_ranking | Rank kozak initiation sequences |
| kozakSequenceScore | Make a score for each ORFs start region by proximity to Kozak |
| lastExonEndPerGroup | Get last end per granges group |
| lastExonPerGroup | Get last exon per GRangesList group |
| lastExonStartPerGroup | Get last start per granges group |
| length-covRleList-method | length covRleList |
| length-covRle-method | length covRle |
| lengths-covRleList-method | lengths covRleList |
| lengths-covRle-method | lengths covRle |
| libFolder | Get ORFik experiment library folder |
| libFolder-experiment-method | Get ORFik experiment library folder |
| libNames | Get library name variants |
| 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 |
| mainNames | Get main name from variant name |
| makeExonRanks | Make grouping by exons ranks |
| makeORFNames | Make ORF names per orf |
| makeSummarizedExperimentFromBam | Make a count matrix from a library or experiment |
| makeTxdbFromGenome | Make txdb from genome |
| mapToGRanges | Map orfs to genomic coordinates |
| matchColors | Match coloring of coverage plot |
| matchNaming | Match naming of GRangesList |
| matchSeqStyle | A wrapper for seqlevelsStyle |
| 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... |
| model.matrix-experiment-method | Get experiment design model matrix |
| name | Get name of ORFik experiment |
| name-experiment-method | Get name of ORFik experiment |
| nrow-experiment-method | Internal nrow function for ORFik experiment Number of runs in... |
| numCodons | Get number of codons |
| numExonsPerGroup | Get list of the number of exons per group |
| ofst_merge | Merge multiple ofst file |
| optimizedTranscriptLengths | Load length and names of all transcripts |
| optimized_txdb_path | Get path for optimization files for txdb |
| optimizeReads | Find optimized subset of valid reads |
| optimizeTranscriptRegions | Make optimized GRangesList objects saved to disc |
| orfFrameDistributions | Find shifted Ribo-seq frame distributions |
| orfID | Get id's for each orf |
| ORFik-package | ORFik for analysis of open reading frames. |
| ORFikQC | A post Alignment quality control of reads |
| ORFik.template.experiment | An ORFik experiment to see how it looks |
| ORFik.template.experiment.zf | An ORFik experiment to see how it looks |
| orfScore | Get ORFscore for a GRangesList of ORFs |
| organism-experiment-method | Get ORFik experiment organism |
| outputLibs | Output NGS libraries to R as variables |
| pasteDir | A paste function for directories Makes sure slashes are... |
| pcaExperiment | Simple PCA analysis |
| percentage_to_ratio | Convert percentage to ratio of 1 |
| plotHelper | Helper function for coverage plots |
| pmapFromTranscriptF | Faster pmapFromTranscript |
| pmapToTranscriptF | Faster pmapToTranscript |
| prettyScoring | Prettify scoring name |
| pseudo.transform | Transform object |
| pSitePlot | Plot area around TIS as histogram |
| QC_count_tables | Create count table info for QC report |
| QCfolder | Get ORFik experiment QC folder path |
| QCfolder-experiment-method | Get ORFik experiment QC folder path |
| QCplots | Correlation and coverage plots for ORFikQC |
| QCreport | A post Alignment quality control of reads |
| QCstats | Load ORFik QC Statistics report |
| QCstats.plot | Make plot of ORFik QCreport |
| r | strandMode covRle |
| rankOrder | ORF rank in transcripts |
| r-covRle-method | strandMode covRle |
| readBam | Custom bam reader |
| readBigWig | Custom bigWig reader |
| read.experiment | Read ORFik 'experiment' |
| readLengthTable | Make table of readlengths |
| readWidths | Get read widths |
| readWig | Custom wig reader |
| reassignTSSbyCage | Reassign all Transcript Start Sites (TSS) |
| reassignTxDbByCage | Input a txdb and reassign the TSS for each transcript by CAGE |
| reduceKeepAttr | Reduce GRanges / GRangesList |
| regionPerReadLength | Find proportion of reads per position per read length in... |
| remakeTxdbExonIds | Get new exon ids after update of txdb |
| remove.experiments | Remove ORFik experiment libraries load in R |
| remove.file_ext | Remove file extension of path |
| removeMetaCols | Removes meta columns |
| removeORFsWithinCDS | Remove ORFs that are within cds |
| removeORFsWithSameStartAsCDS | Remove ORFs that have same start site as the CDS |
| removeORFsWithSameStopAsCDS | Remove ORFs that have same stop site as the CDS |
| removeORFsWithStartInsideCDS | Remove ORFs that have start site within the CDS |
| removeTxdbExons | Remove exons in txList that are not in fiveUTRs |
| removeTxdbTranscripts | Remove specific transcripts in txdb List |
| rename.SRA.files | Rename SRA files from metadata |
| repNames | Get replicate name variants |
| resFolder | Get ORFik experiment main output directory |
| resFolder-experiment-method | Get ORFik experiment main output directory |
| restrictTSSByUpstreamLeader | Restrict extension of 5' UTRs to closest upstream leader end |
| revElementsF | Reverse elements within list |
| reverseMinusStrandPerGroup | Reverse minus strand |
| ribo_fft | Get periodogram data per read length |
| ribo_fft_plot | Get periodogram plot per read length |
| 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) |
| rnaNormalize | Normalize a data.table of coverage by RNA seq per position |
| runIDs | Get SRR/DRR/ERR run ids from ORFik experiment |
| runIDs-experiment-method | Get SRR/DRR/ERR run ids from ORFik experiment |
| save.experiment | Save 'experiment' to disc |
| savePlot | Helper function for writing plots to disc |
| scaledWindowPositions | Scale (bin) windows to a meta window of given size |
| scoreSummarizedExperiment | Helper function for makeSummarizedExperimentFromBam |
| seqinfo-covRleList-method | Seqinfo covRle Extracted from forward RleList |
| seqinfo-covRle-method | Seqinfo covRle Extracted from forward RleList |
| seqinfo-experiment-method | Seqinfo ORFik experiment Extracted from fasta genome index |
| seqlevels-covRleList-method | Seqlevels covRleList Extracted from forward RleList |
| seqlevels-covRle-method | Seqlevels covRle Extracted from forward RleList |
| seqlevels-experiment-method | Seqlevels ORFik experiment Extracted from fasta genome index |
| seqnames-experiment-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-covRleList-method | covRleList show definition |
| show-covRle-method | covRle show definition |
| show-experiment-method | experiment show definition |
| simpleLibs | Converted format of NGS libraries |
| sortPerGroup | Sort a GRangesList |
| splitIn3Tx | Create binned coverage of transcripts, split into the 3... |
| stageNames | Get stage name variants |
| 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... |
| 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... |
| stopCodons | Get the Stop codons (3 bases) from a GRangesList of 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-covRleList-method | strandMode covRle |
| strandMode-covRle-method | strandMode covRle |
| strandPerGroup | Get list of strands per granges group |
| subsetCoverage | Subset GRanges to get coverage. |
| subsetToFrame | Subset GRanges to get desired frame. |
| sum-covRle-method | sum covRle |
| symbols | Get ORFik experiment QC folder path |
| symbols-experiment-method | Get ORFik experiment QC folder path |
| te.plot | Translational efficiency plots |
| te_rna.plot | Translational efficiency plots |
| te.table | Create a TE table |
| tile1 | Tile each GRangesList group to 1-base resolution. |
| tissueNames | Get tissue name variants |
| topMotif | TOP Motif detection |
| TOP.Motif.ecdf | TOP Motif ecdf plot |
| transcriptWindow | Make 100 bases size meta window for all libraries in... |
| transcriptWindow1 | Meta coverage over all transcripts |
| transcriptWindowPer | Helper function for transcriptWindow |
| translationalEff | Translational efficiency |
| trim_detection | Add trimming info to QC report |
| 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... |
| 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 |
| updateTxdbRanks | Update exon ranks of exon data.frame inside txdb object |
| updateTxdbStartSites | Update start sites of leaders |
| upstreamFromPerGroup | Get rest of objects upstream (inclusive) |
| upstreamOfPerGroup | Get rest of objects upstream (exclusive) |
| validateExperiments | Validate ORFik 'experiment' |
| validGRL | Helper Function to check valid GRangesList input |
| validSeqlevels | Helper function to find overlaping seqlevels |
| 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... |
| windowPerTranscript | Get a binned coverage window per transcript |
| xAxisScaler | Scale x axis correctly |
| yAxisScaler | Scale y axis correctly |
