Ctrl+K

regdiffusion.data.load_atlas_microglia

regdiffusion.data.load_atlas_microglia#

regdiffusion.data.load_atlas_microglia(data_dir='data') → AnnData[source]#

Load single cell for microglia from Broad Institute SCP795

Data Source: https://singlecell.broadinstitute.org/single_cell/study/SCP795/a-transcriptomic-atlas-of-the-mouse-cerebellum#study-summary

Paper: A transcriptomic atlas of mouse cerebellar cortex comprehensively defines cell types

Paper Link: https://www.nature.com/articles/s41586-021-03220-z

Raw data is count data. We select all genes that have non-zero expression. We also removed all gene models, Mitochondrial genes, and ribosome genes. We used log-plus-one to transform the count data.

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)

Contents