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regdiffusion.data.load_hammond_microglia

regdiffusion.data.load_hammond_microglia#

regdiffusion.data.load_hammond_microglia(data_dir='data')[source]#

Load single cell for microglia from Hammond Microglia dataset

Data Source: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121654

Paper: Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes Paper Link: https://www.cell.com/immunity/fulltext/S1074-7613(18)30485-0

IMPORTANT! This is not the complete data from the study. We only selected data from the 4 adult male mouses at P100. Here are their accession IDs.

GSM3442026 P100 male no 1 GSM3442027 P100 male no 2 GSM3442030 P100 male no 3 GSM3442031 P100 male no 4

Raw data has already been log transformed. We select all genes that have non-zero expression. We also removed all gene models, Mitochondrial genes, and ribosome genes.

The output is an AnnData object where rows are cells and columns are genes.

Parameters:

  • data_dir (str) – Parent directory to save and load the data. If the path

  • exist (does not)

  • a (it will be created. Data will be saved in)

  • path. (subdirectory under the provided)

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