Repository for generating results in the manuscript "ICAT: A Novel Algorithm to Robustly Identify Cell States Following Perturbations in Single Cell Transcriptomes"
This analysis was run on a high performance cluster with a CentOS operating system.
It is not guaranteed to run on your system out-of-the-box.
To reproduce analysis, simply unzip the archived data files in the archived_data.tar.gz
file, install the conda environment using either the environment.yaml or spec-file.txt
files, activate the environemnt with the command, conda activate icat, and finally
run the pipeline using snakemake (i.e. simply execute snakemake in the terminal)