transcript2gene() to map Ensembl/GENCODE
transcript identifiers to gene ids or namesaggregate_transcripts() to sum a transcript-level
matrix to gene leveldetect_species() and detect_release()
accept transcript identifiersgene_lengths()/stream_exon_lengths() to fetch
exon-union gene lengthsstream_homologies() to read older Compara dumps
that have no is_high_confidence column;
high_confidence is then NA.entrez_ids() no longer fails on identifiers dated
before release 85, which has no cross-reference filesgeneid2name() and correct_genenames()
(renamed from correct_names()) also accept a matrix, sparse
matrix or data frame, replacing row names in place instead of returning
a vector.GeneID2Name(), MitoGenes(),
CorrectGeneNames(), and so on).detect_species_names() infers species and annotation
build from gene symbols alone, no identifiers needed, using an index
from build_symbol_index().First release.