Software and Tools

To facilitate interactions between computational projects and experimental projects, and to ensure timely dissemination of resources, we maintain a Core for Data Integration. This core provides initial processing of complex data sets, and dissemination of them and computational tools developed in their analysis.

We aim to make all data, software, and results generated by the Stanford CCSB readily available to all researchers.

Data Tools

Performs sparse canonical correlation analysis.

Implementation: Excel plug-in
Contact: Rob Tibshirani, PhD

Manage, analyze, and share flow cytometry data over the web.

Implementation: Web Platform
Contact: Help desk (

Supplementary materials  related to the paper: Anchang et al., (2018) DRUG-NEM: Optimizing drug combinations using single-cell perturbation response to account for intratumoral heterogeneity,  accepted.

ContactBenedict Anchang, PhD

An optimized individualized drug combination strategy for intratumoral heterogeneity using single-cell data.

Implementation: R
Contact: Please request access by sending an email to Benedict Anchang, PhD

Performs module network reconstruction.

Implementation: Matlab
Contact: Daphne Koller, PhD

Performs penalized multivariate analysis.

Implementation: R
Contact: Daniela Witten, PhD

Subgroup-specific gene-centering method to perform molecular subtyping on a study cohort.

Implementation: R
Contact: Xi Zhao, PhD