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@SUwonglab The WH Wong lab at Stanford

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    25 repositories

    • IMED

      Public
      IMED is a statistical framework to perform Integrative Mutation and Expression analysis for Driver detection.
      R
      •1•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • carrier-stat

      Public
      Carrier statistic is a statistical framework to prioritize disease-related rare variants by integrating gene expression data
      R
      •
      MIT License
      •1•3•0•0•Updated Feb 18, 2026Feb 18, 2026

    • ProVADA

      Public
      ProVADA: conditional variant generation via ensemble-guided test-time steering
      Jupyter Notebook
      •0•5•0•0•Updated Dec 31, 2025Dec 31, 2025

    • PECA

      Public
      PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
      dnase-seqrna-seqgene-expression
      dnase-seqrna-seqgene-expressionatac-seqgene-regulatory-networkchromatin-accessibiity
      MATLAB
      •8•45•6•1•Updated Oct 7, 2025Oct 7, 2025

    • cRegulon

      Public
      cRegulon is an optimization model to identify combinatorial regulon from single cell expression and chromatin accessibility data.
      combinatorial-regulationtf-modulecell-type-annotation
      combinatorial-regulationtf-modulecell-type-annotationtf-combination
      Python
      •
      GNU General Public License v3.0
      •1•7•0•0•Updated Sep 28, 2025Sep 28, 2025

    • rss-net

      Public
      RSS-NET: Regression with Summary Statistics exploiting Network Topology
      projects
      projects
      R
      •
      MIT License
      •4•19•0•0•Updated Apr 23, 2025Apr 23, 2025

    • arcsv

      Public
      Complex structural variant detection from WGS data
      genomicsvariant-callingstructural-variation
      genomicsvariant-callingstructural-variation
      Python
      •
      MIT License
      •9•31•0•1•Updated Jan 10, 2025Jan 10, 2025

    • AD-genomicLLM

      Public
      Associating genotype to imaging and clinical phenotypes of Alzheimer’s disease by leveraging genomic large language model
      Python
      •
      MIT License
      •1•3•0•0•Updated Oct 25, 2024Oct 25, 2024

    • CausalEGM

      Public
      A General Causal Inference Framework by Encoding Generative Modeling
      generative-modelcausalitycausal-inference
      generative-modelcausalitycausal-inferencetreatment-effectsdeep-generative-modelcausal-machine-learning
      Python
      •11•74•1•0•Updated Jun 1, 2024Jun 1, 2024

    • m2h-ele

      Public
      Sequence-conserved Enhancer-like Elements
      Shell
      •
      MIT License
      •1•5•0•0•Updated Jan 2, 2024Jan 2, 2024

    • TimeReg

      Public
      time course regulatory analysis from paired gene expression and chromatin accessibility time course data
      MATLAB
      •0•11•4•0•Updated Nov 10, 2023Nov 10, 2023

    • Roundtrip

      Public
      Roundtrip: a deep generative neural density estimator
      Python
      •
      MIT License
      •14•1•0•0•Updated Apr 12, 2023Apr 12, 2023

    • scDEC

      Public
      Simultaneous deep generative modeling and clustering of single cell genomic data
      Python
      •
      MIT License
      •7•0•0•0•Updated Nov 14, 2022Nov 14, 2022

    • CoupledNMF

      Public
      Coupled clustering of single cell genomic data
      rna-seqatac-seqsingle-cell
      rna-seqatac-seqsingle-cellclustering-methodsnon-negative-matrix-factorization
      Python
      •1•13•2•0•Updated Sep 21, 2021Sep 21, 2021

    • sc-compReg

      Public
      R package for single-cell comparative regulatory analysis
      scrna-seqscatac-seqcomparative-regulatory-analysis
      scrna-seqscatac-seqcomparative-regulatory-analysis
      R
      •
      GNU General Public License v3.0
      •5•10•4•0•Updated Jun 26, 2021Jun 26, 2021

    • R_utils

      Public
      Useful util R functions
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 12, 2021May 12, 2021

    • OpenCausal

      Public
      A method for scoring the cell-type specific impacts of non-coding variants in personal genomes
      Python
      •
      MIT License
      •3•0•0•0•Updated Jun 22, 2020Jun 22, 2020

    • vPECA

      Public
      MATLAB
      •0•2•1•0•Updated May 9, 2020May 9, 2020

    • DeepCAGE

      Public
      A deep densely connected convolutional network for predicting chromatin accessibility with attention on gene expression
      Python
      •
      MIT License
      •3•0•0•0•Updated May 8, 2020May 8, 2020

    • enrichTF

      Public
      Bioconductor package enrichTF: Transcription Factors Enrichment Analysis
      R
      •4•0•0•0•Updated Mar 28, 2020Mar 28, 2020

    • pipeFrame

      Public
      Bioconductor/R package pipeFrame: Pipeline framework for bioinformatics in R
      R
      •2•0•0•0•Updated Dec 30, 2019Dec 30, 2019

    • scABC

      Public
      atac-seqsingle-cellsingle-cell-atac-seq
      atac-seqsingle-cellsingle-cell-atac-seq
      HTML
      •5•21•3•0•Updated Jul 3, 2019Jul 3, 2019

    • DC3

      Public
      Python
      •3•4•2•0•Updated Feb 25, 2019Feb 25, 2019

    • DeepTACT

      Public
      DeepTACT: predicting three-dimensional chromatin contacts via bootstrapping deep learning
      Python
      •6•0•0•0•Updated Feb 1, 2019Feb 1, 2019

    • COSINE

      Public
      COSINE is an aligner tool for mapping long noisy reads.
      Shell
      •1•5•2•0•Updated May 16, 2017May 16, 2017
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