Updated 9 Dec 2022
This folder contains R scripts to process different single-cell RNA-seq datasets from the Broad Institute database (https://singlecell.broadinstitute.org/single_cell/study/SCPxxx). Normalized expression data should be manually downloaded.
Only SCP548 has been tested for use with scTenifoldKnk, using ALDOA as the knockout gene. The scTenifold raw outputs are in /exports/cmvm/eddie/eb/groups/baillielab2/Nureen/scKO_sepsis_o/. Final report is available as an HTML document.
sc_plotting.py is a modified plotting script from the scTenifoldpy package (version 0.1.3) to override default plot settings.