Raw data is stored in "data/" and the prepared data is saved to "modeling_data/". (The "cache/" directory is for saving intermediate data of analyses.) See the README in the "data/" for instructions to download the raw data for this project.
A single Snakemake workflow prepares all of the data. It can be run using the following command in the root directory of the project.
conda activate speclet_smk
make mungeIf running on O2, the jobs can be parallelized over the HPC cluster using the following command, instead.
make munge_o2Below is the DAG of the pipeline (scaled down to just 5 cell lines).
