Software
Open-source software, tools, and resources developed by members in Chong Wu Lab.
Our group is strongly committed to open science and reproducible research. We actively develop and maintain robust, validated, open-source software, primarily as R packages, implementing our novel statistical methodologies. These tools aim to make complex methods accessible to the broader research community.
A significant contribution is the Global Causal Biomarker Hub (GCB Hub), a comprehensive resource offering pre-computed biomarker prediction models and association results to facilitate downstream validations.
Featured Software Repositories
Below are selected highlights of our software packages and resources available on GitHub. For the most up-to-date versions and comprehensive lists, please visit the individual repositories and the ChongWuLab GitHub page linked below.
Software Tutorials & Guides
We provide detailed tutorials and guides for selected software packages to help users get started and utilize their full capabilities. These tutorials are hosted on our previous site and will open in a new tab.
- glmtlp: View Tutorial
R package for implementing the truncated lasso penalty under a generalized linear model framework. Similar to glmnet but supports non-convex penalties. - IWAS (Imaging-Wide Association Study): View Tutorial
A software for implementing Imaging-Wide Association Studies. (Associated paper: Xu et al., NeuroImage 2017) - TWAS-aSPU: View Tutorial
A powerful gene-based association test integrating eQTL data with GWAS data (individual-level or summary statistics). (Associated paper: Xu et al., Genetics 2017) - aSPUpath2: View Tutorial
A pathway-based method integrating eQTL data with GWAS summary statistics, extending TWAS to pathway analysis. (Associated paper: Wu & Pan, Genetic Epidemiology 2018) - egmethyl: View Tutorial
A gene-based test integrating enhancer-promoter interactions and DNA methylation data with GWAS summary data. (Associated paper: Wu & Pan, Bioinformatics 2019)
Explore All Lab Software
Discover all software, code, and resources developed by our lab members on the official ChongWuLab GitHub organization page: