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.