abagen.fetch_microarray

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

Downloads the Allen Human Brain Atlas microarray expression dataset

Parameters:

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

  • donors (list, optional) – List of donors to download; can be either donor number or UID. Can also specify ‘all’ to download all available donors. Default: 12876

  • 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

  • convert (bool, optional) – Whether to convert downloaded CSV files into parquet format for faster loading in the future; only available if fastparquet and python- snappy are installed. Default: True

  • n_proc (int, optional) – Number of processes to parallelize download if multiple donors are specified. Default: 1

Returns:

data – Two-level nested dictionary, where top-level keys are donor IDs and second-level keys are [‘microarray’, ‘ontology’, ‘pacall’, ‘probes’, ‘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.