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A B C D E F G H I K L M N O P R S T U V W
| 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. |
| 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 |
| 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 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 |
| coverageByWindow | Compute coverage for every GRangesList subset. |
| coveragePerTiling | Get coverage per group |
| 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. |
| extendLeaders | Extend the leaders transcription start sites. |
| extendsTSSexons | Extend first exon of each transcript with length specified |
| filterCage | Filter peak of cage-data by value |
| findCageUTRFivelen | Get length of leaders ordered after oldTxNames |
| findFa | Convenience wrapper for Rsamtools FaFile |
| 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. |
| 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 counts |
| fractionLength | Fraction Length |
| fread.bed | Load bed file as GRanges. |
| getStartStopWindows | Get Start and Stop codon within specified windows over CDS. |
| groupGRangesBy | Group GRanges |
| gSort | Sort a GRangesList, helper. |
| hasHits | Hits from reads |
| 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 |
| 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 |
| 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 |
| longestORFs | Get longest ORF per stop site |
| makeExonRanks | Make a meta column with exon ranks |
| makeORFNames | Make ORF names per orf |
| mapToGRanges | Map orfs to genomic coordinates |
| matchNaming | Match naming of GRangesList |
| metaWindow | Calculate metaplot coverage of reads around input GRangesList object. |
| numExonsPerGroup | Get list of the number of exons per group |
| orfID | Get id's for orf |
| ORFik | ORFik for analysis of open reading frames. |
| orfScore | Get ORFscore for a GRangesList of ORFs |
| overlapsToCoverage | Get overlaps and convert to coverage list |
| parseCigar | Shift ribo-seq reads using cigar string |
| pmapFromTranscriptF | Faster more secure version of mapFromTranscripts |
| rankOrder | ORF rank in transcripts |
| readWidths | Get RiboSeq widths |
| reassignTSSbyCage | Reassign all Transcript Start Sites (TSS) |
| reassignTxDbByCage | Input a txdb and reassign the TSS for each transcript by CAGE |
| reduceKeepAttr | Reduce GRanges / GRangesList |
| regroupRleList | Regroup rle from GRangesList |
| remakeTxdbExonIds | Get new exon ids |
| removeMetaCols | Removes meta columns |
| removeTxdbExons | Remove exons in txList that are not in fiveUTRs |
| restrictTSSByUpstreamLeader | Restrict extension of 5' UTRs to closest upstream leader end |
| ribosomeReleaseScore | Ribosome Release Score (RRS) |
| ribosomeStallingScore | Ribosome Stalling Score (RSS) |
| riboTISCoverageProportion | Find proportion of reads per position in ORF TIS window |
| seqnamesPerGroup | Get list of seqnames per granges group |
| shiftFootprints | Shift footprints by selected offsets |
| sortPerGroup | Sort a GRangesList |
| startCodons | Get the Start codons(3 bases) from a GRangesList of orfs grouped by orfs |
| startDefinition | Returns start definitions |
| startRegionString | Get -20,20 start region as DNA characters per gr 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 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. |
| subset_to_frame | Subset GRanges to get desired frame. GRanges object should be beforehand tiled to size of 1. This subsetting takes account for strand. |
| tile1 | Tile a GRangesList by 1 |
| translationalEff | Translational efficiency |
| txLen | Get transcript lengths |
| txNames | Get transcript names from orf names |
| txNamesWithLeaders | Get the transcripts that have minimum lengths of leaders and cds. |
| 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 |
| updateTxdbStartSites | Update start sites of leaders |
| upstreamFromPerGroup | Get rest of objects upstream (inclusive) |
| upstreamOfPerGroup | Get rest of objects upstream (exclusive) |
| validGRL | Helper Function to check valid GRangesList input |
| widthPerGroup | Get list of widths per granges group |
| windowPerGroup | Get window region of tx around point of gr |