basesDifferent | Calculate the number of bases that are different between two... |
constructAlternativeEvents | Construct alternative transcription events form a list of... |
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... |
filterTranscriptMetadata | Prepare transcript metadata before extending truncated... |
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... |
markLongestTranscripts | 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. |
transcriptsToAnnotations | Convert list of exons to a transcript annotations that can be... |
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