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A B C D E F G H I K L M N O P Q R S T U V W X Y
| ORFik-package | ORFik for analysis of open reading frames. |
| addCdsOnLeaderEnds | Extends leaders downstream |
| addNewTSSOnLeaders | Add cage max peaks as new transcript start sites for each 5' leader (*) strands are not supported, since direction must be known. |
| allFeaturesHelper | Calculate the features in computeFeatures |
| assignAnnotations | Overlaps GRanges object with provided annotations. |
| assignFirstExonsStartSite | Reassign the start positions of the first exons per group in grl |
| assignLastExonsStopSite | Reassign the stop positions of the last exons per group |
| 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 |
| bamVarName | Get library variable names from ORFik 'experiment' |
| bamVarNamePicker | Get variable name per filepath in experiment |
| bedToGR | Converts different type of files to Granges |
| 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 |
| computeFeatures | Get all possible features in ORFik |
| computeFeaturesCage | Get all possible features in ORFik |
| convertToOneBasedRanges | Convert a GRanges Object to 1 width reads |
| countOverlapsW | CountOverlaps with weights |
| countTable | Extract count table directly from experiment |
| coverageByTranscriptW | Remake of coverageByTranscript |
| 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 |
| create.experiment | Create a template for new ORFik 'experiment' |
| defineIsoform | Overlaps GRanges object with provided annotations. |
| defineTrailer | Defines trailers for ORF. |
| detectRibosomeShifts | Detect ribosome shifts |
| disengagementScore | Disengagement score (DS) |
| distToCds | Get distances between ORF ends and starts of their transcripts cds. |
| distToTSS | Get distances between ORF Start and TSS of its transcript |
| downstreamFromPerGroup | Get rest of objects downstream (inclusive) |
| downstreamN | Restrict GRangesList |
| downstreamOfPerGroup | Get rest of objects downstream (exclusive) |
| entropy | Calucalte entropy value of overlapping input reads per GRanges. |
| experiment | experiment class definition |
| experiment-class | experiment class definition |
| export.bed12 | Export as bed12 format |
| export.bedo | Store GRanges object as .bedo |
| extendLeaders | Extend the leaders transcription start sites. |
| extendsTSSexons | Extend first exon of each transcript with length specified |
| extendTrailers | Extend the Trailers transcription stop sites |
| filterCage | Filter peak of cage-data by value |
| 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 positions. |
| findMaxPeaks | Find max peak for each transcript, returns as data.table, without names, but with index |
| findNewTSS | Finds max peaks per trancsript from reads in the cagefile |
| findORFs | Find Open Reading Frames. |
| findORFsFasta | Finds Open Reading Frames in fasta files. |
| findUORFs | Find upstream ORFs from transcript annotation |
| findWigPairs | Find pair of forward and reverse strand wig files |
| firstEndPerGroup | Get first end per granges group |
| firstExonPerGroup | Get first exon per GRangesList group |
| firstStartPerGroup | Get first start per granges group |
| floss | Fragment Length Organization Similarity Score |
| fpkm | Create normalizations of overlapping read counts. |
| fpkm_calc | Create normalizations of read counts |
| fractionLength | Fraction Length |
| fread.bed | Load bed file as GRanges. |
| gcContent | Get GC content |
| getNGenesCoverage | Get number of genes per coverage table |
| getWeights | Get weights from a subject GenomicRanges object |
| groupGRangesBy | Group GRanges |
| groupings | Get number of ranges per group as an iterator |
| gSort | Sort a GRangesList, helper. |
| hasHits | Hits from reads |
| import.bedo | Load GRanges object from .bedo |
| initiationScore | Get initiation score for a GRangesList of ORFs |
| insideOutsideORF | Inside/Outside score (IO) |
| is.grl | Helper function to check for GRangesList |
| is.gr_or_grl | Helper function to check for GRangesList or GRanges class |
| is.ORF | Check if all requirements for an ORFik ORF is accepted. |
| is.range | Helper function to check for ranged object |
| isInFrame | Find frame for each orf relative to cds |
| isOverlapping | Find frame for each orf relative to cds |
| isPeriodic | Find if there is periodicity in the vector |
| kozakHeatmap | Make sequence region heatmap relative to scoring |
| 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 |
| libraryTypes | Which type of library type in 'experiment'? |
| 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 |
| makeExonRanks | Make grouping by exons ranks |
| makeORFNames | Make ORF names per orf |
| makeSummarizedExperimentFromBam | Make a count matrix from a library or experiment |
| mapToGRanges | Map orfs to genomic coordinates |
| matchColors | Match coloring of coverage plot |
| matchNaming | Match naming of GRangesList |
| matchSeqStyle | A wrapper for seqlevelsStyle |
| metaWindow | Calculate meta-coverage of reads around input GRanges/List object. |
| nrow-method | Internal nrow function for ORFik experiment Number of runs in experiment |
| numCodons | Get number of codons |
| numExonsPerGroup | Get list of the number of exons per group |
| optimizeReads | Find optimized subset of valid reads |
| orfID | Get id's for each orf |
| ORFik | ORFik for analysis of open reading frames. |
| ORFikQC | A post Alignment quality control of reads |
| orfScore | Get ORFscore for a GRangesList of ORFs |
| outputLibs | Output bam/bed/bedo/wig files to R as variables |
| parseCigar | Shift ribo-seq reads using cigar string |
| pasteDir | A paste function for directories Makes sure slashes are corrected, and not doubled. |
| plotHelper | Helper function for coverage plots |
| pmapFromTranscriptF | Faster pmapFromTranscript |
| pmapToTranscriptF | Faster pmapToTranscript |
| prettyScoring | Prettify scoring name |
| pSitePlot | Plot area around TIS as histogram |
| QCplots | Correlation and coverage plots for ORFikQC |
| rankOrder | ORF rank in transcripts |
| read.experiment | Read ORFik 'experiment' |
| readBam | Custom bam reader |
| 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 |
| remakeTxdbExonIds | Get new exon ids after update of txdb |
| remove.experiments | Remove bam/bed/wig files load in R as variables |
| 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 |
| restrictTSSByUpstreamLeader | Restrict extension of 5' UTRs to closest upstream leader end |
| ribosomeReleaseScore | Ribosome Release Score (RRS) |
| ribosomeStallingScore | Ribosome Stalling Score (RSS) |
| rnaNormalize | Normalize a data.table of coverage by RNA seq per position |
| 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 |
| seqnamesPerGroup | Get list of seqnames per granges group |
| shiftFootprints | Shift footprints by selected offsets |
| shiftFootprintsByExperiment | Shift footprints of each file in experiment |
| show-method | experiment show definition |
| simpleLibs | Will make a simplified version of NGS libraries |
| sortPerGroup | Sort a GRangesList |
| splitIn3Tx | Create binned coverage of transcripts, split into the 3 parts. |
| 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 |
| stopSites | Get the stop sites from a GRangesList of orfs grouped by orfs |
| strandBool | Get logical list of strands |
| strandPerGroup | Get list of strands per granges group |
| subsetCoverage | Subset GRanges to get coverage. |
| subsetToFrame | Subset GRanges to get desired frame. |
| tile1 | Tile each GRangesList group to 1-base resolution. |
| TOP.Motif.ecdf | TOP Motif ecdf plot |
| transcriptWindow | Make 100 bases size meta window for all libraries in experiment |
| transcriptWindowPer | Helper function for transcriptWindow |
| translationalEff | Translational efficiency |
| 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 |
| uniqueGroups | Get the unique set of groups in a GRangesList |
| uniqueOrder | Get unique ordering for GRangesList groups |
| unlistGrl | Safe unlist |
| 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 window |
| windowPerTranscript | Get a binned coverage window per transcript |
| xAxisScaler | Scale x axis correctly |
| yAxisScaler | Scale y axis correctly |