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    27 repositories

    • RcppPlanc

      Public
      C++
      •
      GNU General Public License v2.0
      •1•3•2•0•Updated Nov 7, 2024Nov 7, 2024

    • PerturbNet

      Public
      PerturbNet is a deep generative model that can predict the distribution of cell states induced by chemical or genetic perturbation
      Python
      •
      GNU General Public License v3.0
      •10•29•2•1•Updated Nov 7, 2024Nov 7, 2024

    • liger

      Public
      R package for integrating and analyzing multiple single-cell datasets
      rsingle-cellnonnegative-matrix-factorization
      R
      •
      GNU General Public License v3.0
      •78•389•19•11•Updated Oct 30, 2024Oct 30, 2024

    • LUMIC

      Public
      Python
      •0•0•0•0•Updated Oct 28, 2024Oct 28, 2024

    • VeloVAE

      Public
      Deep Generative Modeling of RNA Velocity
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •5•34•5•0•Updated Oct 27, 2024Oct 27, 2024

    • cytosignal

      Public
      R
      •1•16•1•0•Updated Oct 24, 2024Oct 24, 2024

    • MultiVelo

      Public
      Multi-omic velocity inference
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•107•16•0•Updated Oct 23, 2024Oct 23, 2024

    • steamer

      Public
      Python
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • welch-lab.github.io

      Public
      Welch Lab
      HTML
      •1.2k•1•0•0•Updated Oct 8, 2024Oct 8, 2024

    • CytoSimplex

      Public
      Simplex plot showing similarity between single-cells and clusters
      R
      •0•1•1•0•Updated Sep 18, 2024Sep 18, 2024

    • 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
      •5•28•8•0•Updated Jul 14, 2024Jul 14, 2024

    • TopoVelo

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 10, 2024Jul 10, 2024

    • ConvNetVAE

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•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•15•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
      •30•0•0•0•Updated Jan 13, 2024Jan 13, 2024

    • AF2_scRNA

      Public
      Jupyter Notebook
      •0•3•0•0•Updated Dec 25, 2023Dec 25, 2023

    • pyCytoSimplex

      Public
      Create simplex plot showing similarity between single-cells and terminal clusters
      Python
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Dec 13, 2023Dec 13, 2023

    • cppliger

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

    • SquiggleNet

      Public
      Python
      •
      MIT License
      •6•20•0•1•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
      •126•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
      •183•1•0•0•Updated Nov 8, 2018Nov 8, 2018