Tutorials#
Running on New Data
Learn how to structure your input data, create configuration files, and run the pipeline on your own single-cell RNA sequencing datasets.
Adding Methods
Understand how to integrate your own transcriptional state discovery method into the CanSig benchmark framework for comparative analysis.
Reproducing Results
Step-by-step instructions for reproducing the benchmark results from our paper, including working with the curated cancer datasets.
Overview of the snakemake pipeline#
The diagram above shows the directed acyclic graph (DAG) of the Snakemake workflow, illustrating how different pipeline components connect and depend on each other.