Repositories list

• iLR

  Public
  iterative logistic regression for marker genes of subtle cell state shifts

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 26, 2025Nov 26, 2025

• popInfer

  Public
  GRN inference with joint scRNA-seq + scATAC-seq data

  R

  •

  MIT License

  •1•4•0•0•Updated Aug 6, 2025Aug 6, 2025

• cancer-systems-immunology

  Public
  Cancer systems immunology reveals myeloid—T cell interactions and B cell activation mediate response to checkpoint inhibition in metastatic breast cancer

  Mathematica

  •0•1•0•0•Updated Jun 20, 2025Jun 20, 2025

• network-logic-EMT

  Public
  GRN models of EMT to investigate the effects of network logic on multistable phenotypes

  MATLAB

  •

  MIT License

  •0•1•0•0•Updated Apr 25, 2025Apr 25, 2025

• stemcell-superhero

  Public
  Interactive cell differentiation model demo

  Julia

  •1•4•0•0•Updated Mar 8, 2025Mar 8, 2025

• dynamicEMT-genes

  Public
  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Feb 13, 2025Feb 13, 2025

• Cell-Cell-Communication

  Public
  Code to accompany the paper: 10.1242/dev.199779

  Jupyter Notebook

  •

  MIT License

  •1•7•0•0•Updated Dec 6, 2024Dec 6, 2024

• scFMC-model

  Public
  Github repository for "Developmental hematopoietic stem cell fate decisions explain clonal dynamics over lifetime"

  Jupyter Notebook

  •0•2•0•0•Updated Dec 2, 2024Dec 2, 2024

• model-discovery

  Public
  Python

  •0•2•0•0•Updated Oct 20, 2024Oct 20, 2024

• ModelingMDSCs

  Public
  Code for Myeloid-derived suppressor cell dynamics control outcomes in the metastatic niche

  Jupyter Notebook

  •1•2•0•0•Updated Apr 24, 2023Apr 24, 2023

• singlecell-parinf

  Public
  Python

  •0•4•0•0•Updated Mar 27, 2023Mar 27, 2023

• RVAgene

  Public
  Recurrent Variational Auto gene encoder

  rnnvaegene-expression-profiles+ 1scrna-seq-analysis

  Jupyter Notebook

  •

  MIT License

  •5•20•2•0•Updated Jan 12, 2023Jan 12, 2023