Reference

Download genome files

download_ensembl_genome	Download Ensembl genome FASTA, transcriptome FASTA, and GTF/GFF3.
download_gencode_genome	Download GENCODE genome FASTA, transcriptome FASTA, GTF, and GFF3.
download_refseq_genome	Download RefSeq genome GFF3 and GTF annotation files.
download_ucsc_genome	Download UCSC genome FASTA and annotation files.

Current versions and builds

current_ensembl_genome_build	Return the current Ensembl genome build for organism.
current_ensembl_version	Return the current Ensembl release version.
current_flybase_version	Return the current FlyBase release version.
current_gencode_genome_build	Return the current GENCODE genome build.
current_gencode_version	Return the current GENCODE release version.
current_refseq_genome_build	Return the current RefSeq genome build for organism.
current_refseq_version	Return the current RefSeq release version.
current_ucsc_genome_build	Return the current UCSC genome build for organism.
current_wormbase_version	Return the current WormBase release version.
detect_organism	Detect the organism from a list of gene/transcript identifiers.
gencode_release_history	Fetch the full GENCODE release history table.

Make genomic objects

EnsemblExons	Ensembl exon annotations.
EnsemblGenes	Ensembl gene annotations.
EnsemblToNcbi	Ensembl-to-NCBI gene identifier mapping.
EnsemblTranscripts	Ensembl transcript annotations.
FlybaseExons	FlyBase exon annotations.
FlybaseGenes	FlyBase gene annotations.
FlybaseTranscripts	FlyBase transcript annotations.
GencodeExons	GENCODE exon annotations.
GencodeGenes	GENCODE gene annotations.
GencodeTranscripts	GENCODE transcript annotations.
GeneToSymbol	Gene identifier-to-symbol mapping.
Hgnc	HGNC (Human Gene Nomenclature Committee) data.
JaxHumanToMouse	JAX human-to-mouse ortholog mapping.
Mgi	MGI (Mouse Genome Informatics) data.
NcbiGeneHistory	NCBI gene history.
NcbiGeneInfo	NCBI gene information.
NcbiToEnsembl	NCBI-to-Ensembl gene identifier mapping.
ProteinToGene	Protein-to-gene identifier mapping.
RefseqExons	RefSeq exon annotations.
RefseqGenes	RefSeq gene annotations.
RefseqTranscripts	RefSeq transcript annotations.
TxToGene	Transcript-to-gene identifier mapping.
UcscExons	UCSC exon annotations.
UcscGenes	UCSC gene annotations.
UcscTranscripts	UCSC transcript annotations.
WormbaseExons	WormBase exon annotations.
WormbaseGenes	WormBase gene annotations.
WormbaseTranscripts	WormBase transcript annotations.
make_ensembl_genes	Create an EnsemblGenes object from a DataFrame.
make_ensembl_genes_from_gtf	Create an EnsemblGenes object from the Ensembl GTF.
make_ensembl_to_ncbi	Create an EnsemblToNcbi mapping from a DataFrame.
make_gene_to_symbol	Create a GeneToSymbol mapping from a DataFrame.
make_granges_from_ensembl	Parse the Ensembl GTF into a BiocPy GenomicRanges object.
make_granges_from_gff	Parse a GFF3 or GTF file into a BiocPy GenomicRanges object.
make_hgnc	Import HGNC (Human Gene Nomenclature Committee) complete set.
make_jax_human_to_mouse	Import JAX human-to-mouse ortholog mapping.
make_mgi	Import Mouse Genome Informatics (MGI) metadata.
make_ncbi_gene_history	Import NCBI gene history for an organism.
make_ncbi_gene_info	Import NCBI gene information for an organism.
make_ncbi_to_ensembl	Create a NcbiToEnsembl mapping from a DataFrame.
make_protein_to_gene_from_ensembl	Map Ensembl protein IDs (ENSP) to gene IDs and gene names.
make_tx_to_gene	Create a TxToGene mapping from a DataFrame.
make_tx_to_gene_from_fasta	Build a TxToGene mapping by parsing FASTA transcript headers.

Gene name mapping

go_terms_per_gene_name	Retrieve GO terms associated with a list of gene names via Ensembl REST.
map_ensembl_release_to_url	Map an Ensembl release version to its archive URL.
map_ensembl_to_gencode	Map an Ensembl release number to the corresponding GENCODE release.
map_gencode_to_ensembl	Map a GENCODE release to its corresponding Ensembl release.
map_gene_names_to_ensembl	Map gene names to Ensembl gene identifiers.
map_gene_names_to_hgnc	Map human gene names (symbols) to HGNC identifiers.
map_gene_names_to_ncbi	Map gene names to NCBI (Entrez) gene identifiers.
map_go_terms	Download the GO OBO file and return a DataFrame of GO term ID and name.
map_human_orthologs	Map gene identifiers to human orthologs via Ensembl REST API.

Version and ID utilities

strip_exon_versions	Strip version suffixes from exon identifiers.
strip_gene_versions	Strip version suffixes from gene identifiers.
strip_transcript_versions	Strip version suffixes from transcript identifiers.
update_gene_symbols	Update gene symbols to current nomenclature.

Data access

import_tx_to_gene

Import transcript-to-gene annotations from a two-column file.