README.md

SpatialQC is a spatial transcriptomic data quality control tool. Available for Linux, Windows and macOS. Run SpatialQC and you'll get an HTML interactive report and clean data.

Install

pip install SpatialQC

Help Documents

SpatialQC -h

See https://mgy520.github.io/SpatialQC/ for detailed help.

Run command:

SpatialQC --adata your.h5ad --markers your_genes.csv

You will get a clean .h5ad file and an HTML interactive report

Sample reports are available in the SpatialQC/paper_example directory.