Man pages for kauralasoo/txrevise
Extend and revise transcript annotatons.
| basesDifferent | Calculate the number of bases that are different between two... |
| calculateBasepairDifference | Calculate the total number of nucleotides that are different... |
| constructAlternativeEvents | Construct alternative transcription events form a list of... |
| constructAlternativeEventsWrapper | Apply constructAlternativeEvents() to an gene_id and metadata... |
| constructEventMetadata | Construct event metadata |
| dataFrameToGRanges | Convert a data frame into a GRanges object |
| extendSingleTranscript | Extend a single transcript in one direction using exons from... |
| extendTranscriptsPerGene | Extend truncated transcripts to the longest annotated... |
| extractGeneData | Extract gene-specifc data from annotations data frame and... |
| fillMissingInternalExons | Fill missing internal exons into alternative transcript start... |
| filterTranscriptMetadata | Prepare transcript metadata before extending truncated... |
| flattenAlternativeEvents | Combine all alternative events into a single list with... |
| identifyTranscriptGroups | Identify two groups of overlapping transcripts that share the... |
| importTranscriptMetadataFromGTF | Extract transcript metadata from Ensembl GTF file |
| indentifyAddedRemovedRegions | Identify regions that are specific to one of the two... |
| listIntersect | Calculate the intersection of a GRangesList object |
| listUnion | Calculate the union of a GRangesList object |
| makeGeneTranscriptFromExons | Construct gene or transcript annotations from exon... |
| markLongestGencodeTranscript | For each gene in a gene metadata data frame, mark the... |
| mergeByMaxDifference | If two transcripts in a GRanges list a are not sufficiently... |
| replaceExtendedTranscripts | Replace extended trancripts in gene-specific data list. |
| reviseAnnotations | reviseAnnotations. |
| splitIntoBatches | Split vector of n elements into batches |
| transcriptsToAnnotations | Convert list of exons to a transcript annotations that can be... |
