Causal Path Lab.

Welcome to Causal Path Lab at UBC and BC Cancer Research.

What We Do

Our primary mission is to do computational biology by developing new statistical learning methods. We do a detective job to hunt for connections between biological entities and ascertain causal effects to reveal "motives" hidden underneath high-dimensional genomic data.

Research Papers

Google Scholar

Research Software (experimental)

legume, Library for Exploring Genomics with Utility functions and Machine learning Essentials, is a family of Rust tools for single-cell and spatial genomics, built on a shared sparse data backend:

  • data-beans: sparse data storage, QC, and simulation
  • lupin: cell type and pathway annotation, trajectories
  • senna: cell and gene embedding
  • chickpea: peak-to-gene linking analysis
  • pinto: spatial transcriptomics
  • faba: RNA variant calling (e.g., m⁶A) from BAM files
  • mung: malignant clone unmixing by copy-number change
  • cocoa: counterfactual differential expression

ASAP, Annotating Single-cell data matrix by Approximate Pseudo-bulk projection:

Other Terminal User Interface Tools

  • paperstack: an app to organize and keep PDF files along with their bibliography information.

  • ohp: an app to view PDF, markdown, and HTML pages in the terminal. It needs a terminal that can display images, such as kitty.