Resources
Setup Computational Environment
Get CCAL Codebase
Workflows
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.
Published
APOBEC-Related Mutational Signature Enrichment Estimation
Onco-GPS