Welcome to CWAS-Plus2 documentation!
CWAS-Plus2 (Category-Wide Association Study) is a data analysis tool designed to conduct rigorous association tests for discovering noncoding associations in complex genomic disorders. It runs category-based burden tests using variants from whole-genome sequencing data and various annotation datasets. CWAS-Plus2 provides a user-friendly interface for efficient hypothesis testing and has promising implications for uncovering the pathophysiology of various genomic disorders.
Here are the reference papers:
An analytical framework for whole genome sequence association studies and its implications for autism spectrum disorder (Werling et al., 2018)
Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder (An et al., 2018)
CWAS-Plus: Estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data (Kim et al., 2024)
CWAS-Plus2 workflow
A. Workflow: Variants extracted from whole-genome sequencing data of samples (sample variant) serve as inputs. B-G. Graphic descriptions of each process in CWAS-Plus2: Red (case) and blue (control) represent the phenotype. F. Representative network pointed by the purple arrow provides an enlarged view of a subset of the network. Node color indicates the direction of the burden in each category (red, case burden; blue, control burden). G. Node color reflects the scale of the normalized z-score, which represents the degree of disease association of the cluster. Darker red indicates a higher association. Node size represents the number of categories within the cluster.
CWAS-Plus2 tutorial
CWAS-Plus2 installation
CWAS-Plus2 requirements
CWAS-Plus2 configuration
CWAS-Plus2 steps
Other useful commands
FAQ
Misc.
Here is the original CWAS repository: sanderslab/cwas