Package: genevintage 0.1.3

Saket Choudhary

genevintage: Detect Annotation Releases and Repair Gene Names

Detects the species and the 'Ensembl' <https://www.ensembl.org> or 'GENCODE' <https://www.gencodegenes.org> annotation release associated with a set of gene or transcript identifiers by scoring them against a bundled fingerprint of each release. Identifiers are then converted to gene names using the matching release. Gene symbols that spreadsheet software turned into dates or numbers ('SEPT9' to '9-Sep') are restored to the spelling of the chosen release. Also retrieves genes by class (mitochondrial, sex-linked, protein-coding, ribosomal, transfer RNA, long non-coding RNA), exon-union gene lengths, 'Entrez' cross-references, and orthologs in another species from 'Ensembl Compara'.

Authors:Saket Choudhary [aut, cre]

genevintage_0.1.3.tar.gz
genevintage_0.1.3.zip(r-4.7-any)genevintage_0.1.3.zip(r-4.6-any)genevintage_0.1.3.zip(r-4.5-any)
genevintage_0.1.3.tgz(r-4.6-any)genevintage_0.1.3.tgz(r-4.5-any)
genevintage_0.1.3.tar.gz(r-4.7-any)genevintage_0.1.3.tar.gz(r-4.6-any)
genevintage_0.1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
genevintage/json (API)

# Install 'genevintage' in R:

install.packages('genevintage', repos = c('https://saketlab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/saketlab/genevintage/issues

Pkgdown/docs site:https://genevintage.saketlab.org

On CRAN:

3.40 score 88 exports 0 dependencies

Last updated from:1a48da0faf (on main). Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	119
source / vignettes	OK	226
linux-release	OK	153
macos-release	OK	132
macos-oldrel	OK	96
windows-devel	OK	92
windows-release	OK	69
windows-oldrel	OK	88
wasm-release	OK	80

Exports:aggregate_transcripts AggregateTranscripts annotate_genes AnnotateGenes build_symbol_index build_symbol_index_from_gtf BuildSymbolIndex BuildSymbolIndexFromGTF coding_genes CodingGenes compare_releases CompareReleases correct_genenames CorrectGeneNames detect_release detect_species detect_species_names DetectRelease DetectSpecies DetectSpeciesNames entrez_ids EntrezIDs fetch_mapping fetch_orthologs fetch_transcripts fetch_xrefs FetchMapping FetchOrthologs FetchTranscripts FetchXrefs gene_biotypes gene_cache gene_ids gene_lengths gene_names GeneBiotypes GeneCache geneid2name GeneID2Name GeneIDs GeneLengths GeneNames genes_by_biotype GenesByBiotype guess_scheme GuessScheme hemoglobin_genes HemoglobinGenes lncrna_genes lncRNAGenes mhc_genes MHCGenes mito_genes MitoGenes noncoding_genes NoncodingGenes ortholog_species orthologs Orthologs OrthologSpecies parse_ens ParseEns qmax_violations QmaxViolations resolve_species ResolveSpecies ribosomal_genes RibosomalGenes rrna_genes rRNAGenes sex_genes SexGenes species_table SpeciesTable stream_exon_lengths stream_gtf stream_homologies stream_transcripts stream_xrefs StreamExonLengths StreamGTF StreamHomologies StreamTranscripts StreamXrefs transcript2gene Transcript2Gene trna_genes tRNAGenes

Dependencies:

How genevintage works

Detecting species | Determining the annotation release | Handling GENCODE and Ensembl | Caution around new releases

Rendered fromhow-it-works.Rmdusingknitr::rmarkdown

Last update: 2026-09-21
Started: 2026-09-21

Help page	Topics
Sum transcript-level counts to gene level	AggregateTranscripts aggregate_transcripts
Everything the annotation knows about a set of genes	AnnotateGenes annotate_genes
Build a compact species/release gene-symbol index from GTF mappings	BuildSymbolIndex build_symbol_index
Fetch GTF mappings and build a symbol index	BuildSymbolIndexFromGTF build_symbol_index_from_gtf
Protein-coding genes	CodingGenes coding_genes
Compare two releases of one annotation	CompareReleases compare_releases
Repair gene symbols a spreadsheet has converted to dates or numbers	CorrectGeneNames correct_genenames
Which Ensembl release a set of identifiers came from	DetectRelease detect_release
Which species a set of identifiers belongs to	DetectSpecies detect_species
Detect species from gene symbols	DetectSpeciesNames detect_species_names
NCBI Entrez identifiers for a set of genes	EntrezIDs entrez_ids
Mapping table for one species and Ensembl release	FetchMapping fetch_mapping
Ortholog table for one species pair and Ensembl release	FetchOrthologs fetch_orthologs
Transcript-to-gene table for one species and release	FetchTranscripts fetch_transcripts
Ensembl gene identifiers and their cross-references, cached	FetchXrefs fetch_xrefs
What biotypes an annotation contains	GeneBiotypes gene_biotypes
Inspect or clear the download cache	GeneCache gene_cache
Gene identifiers for gene names or Entrez identifiers	GeneIDs gene_ids
Exon-union gene lengths for one species and release	GeneLengths gene_lengths
Convert gene identifiers to gene names	GeneNames gene_names
Convert gene identifiers to gene names, detecting species and release	GeneID2Name geneid2name
Genes of a given biotype, or class of biotypes	GenesByBiotype genes_by_biotype
Which identifier scheme a vector of IDs uses	GuessScheme guess_scheme
Hemoglobin subunit genes	HemoglobinGenes hemoglobin_genes
Long non-coding RNA genes	lncRNAGenes lncrna_genes
Major histocompatibility complex genes	MHCGenes mhc_genes
Mitochondrial genes	MitoGenes mito_genes
Non-coding RNA genes	NoncodingGenes noncoding_genes
Species Compara publishes homologies for	OrthologSpecies ortholog_species
Find orthologs of gene identifiers in another species	Orthologs orthologs
Parse Ensembl identifiers into their parts	ParseEns parse_ens
Where the index violates its own ordering invariant	QmaxViolations qmax_violations
Resolve a species name	ResolveSpecies resolve_species
Ribosomal genes	RibosomalGenes ribosomal_genes
Ribosomal RNA genes	rRNAGenes rrna_genes
Sex-chromosome genes	SexGenes sex_genes
Species the index covers, with their common names	SpeciesTable species_table
Exon-union lengths from a GTF, streamed without writing it to disk	StreamExonLengths stream_exon_lengths
Pull gene records out of a GTF without ever writing it to disk	StreamGTF stream_gtf
Stream one species' orthologs against one other species	StreamHomologies stream_homologies
Transcript-to-gene records from a GTF, streamed without writing it to disk	StreamTranscripts stream_transcripts
Stream one cross-reference TSV, keeping the gene-level pairs	StreamXrefs stream_xrefs
Map transcript identifiers to their genes	Transcript2Gene transcript2gene
Transfer RNA genes	tRNAGenes trna_genes

Package: genevintage 0.1.3

genevintage: Detect Annotation Releases and Repair Gene Names

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