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    29 repositories

    • AF2_scRNA

      Public
      Jupyter Notebook
      •0•3•0•0•Updated Aug 1, 2025Aug 1, 2025

    • liger

      Public
      R package for integrating and analyzing multiple single-cell datasets
      rsingle-cellnonnegative-matrix-factorization
      R
      •
      GNU General Public License v3.0
      •79•417•29•11•Updated Jul 23, 2025Jul 23, 2025

    • welch-lab.github.io

      Public
      Welch Lab
      HTML
      •1.3k•1•0•0•Updated Jul 21, 2025Jul 21, 2025

    • RcppPlanc

      Public
      C++
      •
      GNU General Public License v2.0
      •2•7•0•0•Updated Jul 15, 2025Jul 15, 2025

    • libplanc

      Public
      Distributed NMF/NTF Library
      C++
      •
      Other
      •21•2•1•0•Updated Jul 14, 2025Jul 14, 2025

    • PerturbNet

      Public
      PerturbNet is a deep generative model that can predict the distribution of cell states induced by chemical or genetic perturbation
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •11•34•0•1•Updated Jul 10, 2025Jul 10, 2025

    • MultiVeloVAE

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Jul 9, 2025Jul 9, 2025

    • cytosignal

      Public
      R
      •1•18•4•0•Updated Jun 25, 2025Jun 25, 2025

    • pyliger

      Public
      Python package for integrating and analyzing multiple single-cell datasets (A Python version of LIGER)
      pythonsingle-cellnon-negative-matrix-factorizationmulti-omic-integration
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •7•30•9•0•Updated May 16, 2025May 16, 2025

    • VeloVAE

      Public
      Deep Generative Modeling of RNA Velocity
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •7•35•8•0•Updated May 4, 2025May 4, 2025

    • steamer

      Public
      Python
      •0•0•0•0•Updated May 3, 2025May 3, 2025

    • CytoSimplex

      Public
      Simplex plot showing similarity between single-cells and clusters
      R
      •2•5•1•0•Updated Apr 23, 2025Apr 23, 2025

    • TopoVelo

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•6•1•0•Updated Apr 15, 2025Apr 15, 2025

    • pyCytoSimplex

      Public
      Create simplex plot showing similarity between single-cells and terminal clusters
      Python
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Mar 31, 2025Mar 31, 2025

    • LUMIC

      Public
      Python
      •0•1•0•0•Updated Feb 5, 2025Feb 5, 2025

    • MultiVelo

      Public
      Multi-omic velocity inference
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•110•18•0•Updated Oct 23, 2024Oct 23, 2024

    • ConvNetVAE

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•1•0•Updated May 30, 2024May 30, 2024

    • BICCN

      Public
      R
      •1•1•11•1•Updated Apr 19, 2024Apr 19, 2024

    • MichiGAN

      Public
      Learning disentangled representations of single-cell data for high-quality generation
      Python
      •
      GNU General Public License v3.0
      •4•16•1•0•Updated Mar 16, 2024Mar 16, 2024

    • SiNMFiD

      Public
      HTML
      •
      Other
      •1•0•0•0•Updated Mar 15, 2024Mar 15, 2024

    • welch-lab.r-universe.dev

      Public
      0•0•0•0•Updated Mar 15, 2024Mar 15, 2024

    • actions-eleventy

      Public
      GitHub Action for generating a static website with Eleventy
      Shell
      •36•0•0•0•Updated Jan 13, 2024Jan 13, 2024

    • cppliger

      Public
      CMake
      •
      The Unlicense
      •0•0•0•0•Updated Jan 27, 2023Jan 27, 2023

    • SquiggleNet

      Public
      Python
      •
      MIT License
      •6•21•2•0•Updated Oct 29, 2022Oct 29, 2022

    • illustrator_tutorial

      Public
      0•0•0•0•Updated Oct 24, 2022Oct 24, 2022

    • welch-lab.github.io.old

      Public
      HTML
      •2•2•0•2•Updated Oct 6, 2022Oct 6, 2022

    • topologizer

      Public
      Topologizer
      Python
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Sep 16, 2019Sep 16, 2019

    • SnapATAC

      Public
      Single Nucleus Analysis Pipeline for ATAC-seq
      R
      •
      GNU General Public License v3.0
      •132•1•0•0•Updated Apr 27, 2019Apr 27, 2019

    • kepler-mapper

      Public
      KeplerMapper is a Python class for visualization of high-dimensional data and 3-D point cloud data.
      Python
      •
      MIT License
      •185•1•0•0•Updated Nov 8, 2018Nov 8, 2018