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Setup Computational Environment
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Get CCAL Codebase


These workflows are used and updated regularly by the CCAL team. Please use Github Issues for questions or problems that arise when running them.

Works in Progress

Model and Infer

Select features most useful for data decomposition, decompose data into NMF factors, define data states, annotate data states and factors, and visualize annotated factors and states on a map.

Match Pattern

Convert raw RNA-Seq data to a gene expression matrix, compare gene expression of sample groups, run single sample GSEA, compare gene set expression of sample groups.


APOBEC-Related Mutational Signature Enrichment Estimation