Prepare datasets

Datasets should be preprocessed to proceed. scGNN accepts scRNA-seq data format: CSV and 10X

1. Dowmload datasets

CSV format explicitly shows data in plain text. We take an example of Alzheimer’s disease datasets (GSE138852) analyzed in the manuscript.

10X format stores scRNA-seq expression sparsely, so is commonly used for huge datasets. Take an example of liver cellular landscape study from human cell atlas(https://data.humancellatlas.org/)

Example:

CSV format

Take an example of Alzheimer’s disease datasets (GSE138852) analyzed in the manuscript.

mkdir GSE138852
wget -P GSE138852/ https://ftp.ncbi.nlm.nih.gov/geo/series/GSE138nnn/GSE138852/suppl/GSE138852_counts.csv.gz

10X format

Take an example of liver cellular landscape study from human cell atlas(https://data.humancellatlas.org/). Click the download link of ‘homo_sapiens.mtx.zip’ in the page, and get 4d6f6c96-2a83-43d8-8fe1-0f53bffd4674.homo_sapiens.mtx.zip. (It looks like they does not provide direct download link anymore)

mkdir liver
wget -P liver https://data.humancellatlas.org/project-assets/project-matrices/4d6f6c96-2a83-43d8-8fe1-0f53bffd4674.homo_sapiens.mtx.zip
cd liver
unzip 4d6f6c96-2a83-43d8-8fe1-0f53bffd4674.homo_sapiens.mtx.zip
cd ..