CellPathway: Cell type-specific enhancer informs pathway-based approaches for association analysis in whole-genome sequencing studies
CellPathway is a framework that directly tests associations between noncoding variants and cell type–specific pathways defined by enhancer activity.
Please refer to requirements.txt for required packages.
Please refer to CellPathway.ipynb for how to use CellPathway. All inputs and outputs during this example CellPathway run are in the example data folder.
Before running CellPathway, noncoding de novo mutations must be prepared for all samples. We recommend using ANNOVAR to identify and filter rare noncoding variants and to annotate variant pathogenicity using Combined Annotation Dependent Depletion (CADD) scores. These annotated variants serve as the input for downstream cell type–specific pathway analysis in CellPathway.
Typically you will go to the ANNOVAR website, fill in a registration form, and download the package there. When you have requested the ANNOVAR from the website and downloaded it, you will receive a compressed file annovar.latest.tar.gz, you will need to unzip it. Then follow the user guide to install ANNOVAR.
Please follow CADD repository for instructions on how to install and run CADD.