abagen.mouse.fetch_allenref_genes

abagen.mouse.fetch_allenref_genes(entry_type=None, cache=True, data_dir=None, verbose=True)[source]

Loads all genes from Allen Reference database

Parameters:

  • entry_type ({'id', 'acronym', 'name'}, optional) – The type of gene identifier to load. Specifying ‘id’ returns a list of numerical gene IDs, ‘acronym’ returns a list of short-form gene acronyms, and ‘name’ returns full gene names. If not specified, returns a dataframe with all information. Default: None

  • cache (bool, optional) – Whether to use cached gene information (if it exists). Setting to False will overwrite cache. Default: True

  • data_dir (str, optional) – Directory where data should be downloaded and unpacked. Default: $HOME/ abagen-data

  • verbose (bool, optional) – Whether to print status message. Default: True

Returns:

genes – Genes in Allen Reference database

Return type:

list or pandas.DataFrame

Notes

May require internet access to make query to the Allen API (which will take some time); after query is made once the results are cached.