The WH Wong lab at Stanford

CausalEGM

A General Causal Inference Framework by Encoding Generative Modeling

PECA

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

arcsv

Complex structural variant detection from WGS data

scABC

rss-net

Regression with Summary Statistics exploiting Network Topology.

CoupledNMF

Coupled clustering of single cell genomic data

TimeReg

time course regulatory analysis from paired gene expression and chromatin accessibility time course data

sc-compReg

R package for single-cell comparative regulatory analysis

COSINE

COSINE is an aligner tool for mapping long noisy reads.

DC3

m2h-ele

Sequence-conserved Enhancer-like Elements

vPECA

Roundtrip

Roundtrip: a deep generative neural density estimator

BayesGM

A Bayesian approach for generative modeling of high-dimensional data

cRegulon

cRegulon is an optimization model to identify combinatorial regulon from single cell expression and chromatin accessibility data. Topics Resources Readme

DeepCAGE

A deep densely connected convolutional network for predicting chromatin accessibility with attention on gene expression

DeepTACT

DeepTACT: predicting three-dimensional chromatin contacts via bootstrapping deep learning

enrichTF

Bioconductor package enrichTF: Transcription Factors Enrichment Analysis

Epi-PRS

Polygenic prediction by leveraging genomic large language models

OpenCausal

A method for scoring the cell-type specific impacts of non-coding variants in personal genomes

pipeFrame

Bioconductor/R package pipeFrame: Pipeline framework for bioinformatics in R

R_utils

Useful util R functions

scDEC

Simultaneous deep generative modeling and clustering of single cell genomic data