abagen.fetch_rnaseq

abagen.fetch_rnaseq(data_dir=None, donors=None, resume=True, verbose=1)[source]

Downloads RNA-sequencing data from the Allen Human Brain Atlas

Parameters

  • data_dir (str, optional) – Directory where data should be downloaded and unpacked. Default: current directory

  • donors (list, optional) – List of donors to download; can be either donor number or UID. Can also specify ‘all’ to download all available donors (two). Default: 9861

  • resume (bool, optional) – Whether to resume download of a partly-downloaded file. Default: True

  • verbose (int, optional) – Verbosity level (0 means no message). Default: 1

Returns

data – Two-level nested dictionary, where top-level keys are donor IDs and second-level keys are [‘counts’, ‘tpm’, ‘ontology’, ‘genes’, ‘annotation’], where corresponding values are lists of filepaths to downloaded CSV files.

Return type

dict

References

Hawrylycz, M. J., Lein, E. S., Guillozet-Bongaarts, A. L., Shen, E. H., Ng, L., Miller, J. A., … & Abajian, C. (2012). An anatomically comprehensive atlas of the adult human brain transcriptome. Nature, 489(7416), 391.