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    68 repositories

    • MitoEJ-paper-analysis

      Public
      Code for Figures for MitoEJ paper by Yi and Max
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Dec 28, 2024Dec 28, 2024

    • sharp

      Public
      A single-cell demultiplexing pipeline, the sharp (♯)
      Jupyter Notebook
      •
      MIT License
      •1•0•2•0•Updated Dec 15, 2024Dec 15, 2024

    • segger_dev

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Dec 10, 2024Dec 10, 2024

    • progressive-plasticity-crc-metastasis

      Public
      Notebooks for generating figures in "Progressive Plasticity During Colorectal Cancer Metastasis"
      Jupyter Notebook
      •2•10•1•0•Updated Dec 1, 2024Dec 1, 2024

    • Palantir

      Public
      Single cell trajectory detection
      markov-chaindimensionality-reductionscrna-seqtrajectory-generationdiffusion-mapsdifferentiationmanifold-learningsingle-cell-genomicscell-fate-transitionsscrna-seq-analysis
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •52•231•8•0•Updated Nov 30, 2024Nov 30, 2024

    • WassersteinWormhole

      Public
      Transformer Based Embeddings of Wasserstein Distance
      Python
      •
      MIT License
      •1•13•1•1•Updated Nov 4, 2024Nov 4, 2024

    • Brain-metastasis-TME

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

    • ENVI

      Public
      Python
      •
      MIT License
      •6•40•11•1•Updated Oct 16, 2024Oct 16, 2024

    • spectra

      Public
      Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms
      Python
      •
      MIT License
      •18•160•18•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
      •12•46•8•0•Updated Jul 13, 2024Jul 13, 2024

    • 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
      •27•151•26•4•Updated Jun 28, 2024Jun 28, 2024

    • integrateCNV

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 27, 2024Jun 27, 2024

    • cellpose

      Public
      a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •410•1•0•0•Updated May 13, 2024May 13, 2024

    • STAR

      Public
      RNA-seq aligner
      C++
      •
      MIT License
      •508•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
      •40•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
      •2•2•0•0•Updated Jan 14, 2024Jan 14, 2024

    • PrismSpot

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

    • scKINETICS

      Public
      Code for scKINETICS (ISMB 2023)
      expectation-maximizationatac-seqsingle-cell-analysisgene-regulatory-network
      Jupyter Notebook
      •3•21•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
      •30•1•2•0•Updated Sep 19, 2023Sep 19, 2023

    • Treg_depletion_reproducibility

      Public
      Code related to analyses in Glasner, Rose, Sharma, et al Nature Immunology 2023.
      HTML
      •
      MIT License
      •0•2•0•0•Updated Jul 13, 2023Jul 13, 2023

    • SpectraReproducibility

      Public
      Notebooks for reproducing figures in the Spectra paper
      Jupyter Notebook
      •3•7•2•0•Updated Jun 7, 2023Jun 7, 2023

    • ArchR

      Public
      ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
      R
      •
      MIT License
      •140•4•0•0•Updated May 17, 2023May 17, 2023

    • pdac-progression

      Public
      Jupyter Notebook
      •4•10•1•0•Updated Apr 28, 2023Apr 28, 2023

    • wdl-cellranger-arc

      Public
      WDLized Cell Ranger ARC
      WDL
      •
      MIT License
      •1•0•0•0•Updated Apr 21, 2023Apr 21, 2023

    • wdl-cellranger-gex

      Public
      WDLized Cell Ranger GEX
      WDL
      •
      MIT License
      •2•0•0•0•Updated Apr 11, 2023Apr 11, 2023

    • docker-cellranger-arc

      Public
      Dockerized Cell Ranger ARC
      Shell
      •1•0•0•0•Updated Apr 4, 2023Apr 4, 2023