R function for the classification of small insertions and deletions for mutational signature analysis.

ecDNAInspector (ecI) provides a systematic method for ecDNA structural validation and analysis, enabling higher-confidence utilization of sequencing data-based predictions in studies of ecDNA.

Code to reproduce results from "Simulation-Based Inference: A Practical Guide"

Black-box Bayesian inference for agent-based models

Combination of transformers and diffusion models for flexible all-in-one simulation-based inference

Python Gauss-Jordan Algorithm: Solve linear equations and find matrix inverses with ease.

IPython notebooks on Gilbert Strang's MIT course on linear algebra (18.06)

Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling"

Measuring the high-order genome architectures (global folding and checkerboard) from Hi-C experiment

Tumor-normal variant calling workflow using HiFi reads

A tool for somatic structural variant calling using long reads

SCAN2 is a somatic SNV and indel genotyper for single cells amplified by Primary Template-Directed Amplification (PTA)

Code for aging project

UCB EECS126 : probability theory and random processes.

A heterogeneous network embedding based method by integrating genomic data with genes’ biological processes including protein-protein interactions and pathways.

Git repo for CONIPHER tree building

A Statistical Framework for Posterior Profiling Cancer-Driving Sites based on Recurrent Somatic Mutations

Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data

This repository contains the source code of the R package for EvoGeneX, a software to infer the mode of evolution from the gene expression data.

Self-study on Larry Wasserman's "All of Statistics"

Axolotl Regenerative Telencehpalon Interpretation via Spatiotemporal Transcriptomic Atlas

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

GitHub repository for the paper Mitochondrial heteroplasmy improves risk prediction for myeloid neoplasms