Academic Software

Our lab is committed to developing open-source softwares to advance data science research. Below are some of the software projects we have developed with Python and/or R packages.

Statistics

• CausalEGM: A causal inference algorithm that could handle large-scale datasets [Github][Pypi][CRAN][Website].
• Roundtrip: A density estimation algorithm using deep generative neural networks [Github][Pypi].
• scDEC: A method for high-dimensional data clustering/embedding with applications to the scATAC-seq and multiome data [Github].

Computational Biology

• DeepCDR: A graph neural network-based method for the cancer drug response prediction [Github].
• hicGAN: A GAN-based framework for enhancing the resolution of Hi-C data [Github].
• HiChIPdb: The first HiChIP database, containing 262 million interactions across 108 cell types [Database].