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    74 repositories

    • ENVI

      Public
      Jupyter Notebook
      •
      MIT License
      •10•50•12•2•Updated Oct 9, 2025Oct 9, 2025

    • segmentation-tools

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 9, 2025Oct 9, 2025

    • sharp

      Public
      A single-cell demultiplexing pipeline, the sharp (♯)
      Jupyter Notebook
      •
      MIT License
      •1•0•2•0•Updated Oct 1, 2025Oct 1, 2025

    • PLASTRO

      Public
      Plasticity analysis for paired lineage tracing and phenotypic data.
      Python
      •
      MIT License
      •1•0•0•0•Updated Sep 30, 2025Sep 30, 2025

    • WassersteinWormhole

      Public
      Transformer Based Embeddings of Wasserstein Distance
      Python
      •
      MIT License
      •2•20•1•1•Updated Sep 8, 2025Sep 8, 2025

    • picasso

      Public
      Top-down phylogenetic inference from single-cell data
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Aug 29, 2025Aug 29, 2025

    • segger-analysis

      Public
      Notebooks and code for analyzing Segger data
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Aug 14, 2025Aug 14, 2025

    • Palantir

      Public
      Single cell trajectory detection
      markov-chaindimensionality-reductionscrna-seqtrajectory-generationdiffusion-mapsdifferentiationmanifold-learningsingle-cell-genomicscell-fate-transitionsscrna-seq-analysis
      Jupyter Notebook
      •
      MIT License
      •56•268•10•0•Updated Jun 27, 2025Jun 27, 2025

    • BayesPrism

      Public
      A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
      HTML
      •57•0•0•0•Updated May 29, 2025May 29, 2025

    • SpaceFold

      Public
      HTML
      •1•7•1•0•Updated Mar 30, 2025Mar 30, 2025

    • SEACells

      Public
      SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •29•168•30•4•Updated Mar 27, 2025Mar 27, 2025

    • segger_dev

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated Mar 21, 2025Mar 21, 2025

    • supervised-spectra

      Public
      Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
      Jupyter Notebook
      •
      MIT License
      •21•1•0•0•Updated Mar 5, 2025Mar 5, 2025

    • integrateCNV

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 26, 2025Feb 26, 2025

    • MitoEJ-paper-analysis

      Public
      Code for Figures for MitoEJ paper by Yi and Max
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Feb 26, 2025Feb 26, 2025

    • progressive-plasticity-crc-metastasis

      Public
      Notebooks for generating figures in "Progressive Plasticity During Colorectal Cancer Metastasis"
      Jupyter Notebook
      •4•16•6•0•Updated Dec 1, 2024Dec 1, 2024

    • Brain-metastasis-TME

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Oct 30, 2024Oct 30, 2024

    • spectra

      Public
      Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
      Python
      •
      MIT License
      •21•175•24•5•Updated Jul 26, 2024Jul 26, 2024

    • Harmony

      Public
      Harmony framework for connecting scRNA-seq data from discrete time points
      scrna-seqmnnbatch-correctionscrna-seq-analysisdevelopmental-trajecotries
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •13•51•8•1•Updated Jul 13, 2024Jul 13, 2024

    • cellpose

      Public
      a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •528•1•0•0•Updated May 13, 2024May 13, 2024

    • STAR

      Public
      RNA-seq aligner
      C++
      •
      MIT License
      •534•1•0•0•Updated May 10, 2024May 10, 2024

    • benchkit

      Public
      Scripts for managing and processing large number of samples, also providing a CLI.
      0•0•0•0•Updated May 9, 2024May 9, 2024

    • docker-cellranger

      Public
      Dockerized Cell Ranger
      Shell
      •
      MIT License
      •3•0•0•0•Updated May 3, 2024May 3, 2024

    • ecosystem-packages

      Public
      Register pe'er lab packages to scverse ecosystem
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •58•0•0•0•Updated Apr 15, 2024Apr 15, 2024

    • mssi

      Public
      Jupyter Notebook
      •
      MIT License
      •0•3•1•0•Updated Mar 19, 2024Mar 19, 2024

    • cytopus

      Public
      Single cell omics biology annotations
      Jupyter Notebook
      •
      MIT License
      •3•2•0•0•Updated Jan 14, 2024Jan 14, 2024

    • PrismSpot

      Public
      Jupyter Notebook
      •0•3•1•0•Updated Oct 24, 2023Oct 24, 2023

    • scKINETICS

      Public
      Code for scKINETICS (ISMB 2023)
      expectation-maximizationatac-seqsingle-cell-analysisgene-regulatory-network
      Jupyter Notebook
      •3•22•4•0•Updated Oct 23, 2023Oct 23, 2023

    • scing

      Public
      SCING: Single-Cell pIpeliNe Garden (pronounced as "sing" /siŋ/)
      Python
      •
      MIT License
      •3•0•0•0•Updated Oct 5, 2023Oct 5, 2023

    • MERlin

      Public
      MERFISH decoding software
      Python
      •
      MIT License
      •31•1•2•0•Updated Sep 19, 2023Sep 19, 2023