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    • cumulus

      Public
      Cloud-based scalable and efficient single-cell genomics workflows
      WDL
      3668120Updated Feb 17, 2026Feb 17, 2026
    • Backend component of Cumulus for different cloud environments.
      Python
      0211Updated Feb 16, 2026Feb 16, 2026
    • Website of Dr Li's Lab
      HTML
      0000Updated Feb 12, 2026Feb 12, 2026
    • pegasus

      Public
      A tool for analyzing trascriptomes of millions of single cells.
      Python
      2593122Updated Jan 23, 2026Jan 23, 2026
    • pegasusio

      Public
      pegasus io module for reading/writing single-cell genomics data
      Python
      4811Updated Jan 22, 2026Jan 22, 2026
    • Command line tool for submitting WDL jobs to Terra or Cromwell server.
      Python
      0731Updated Jan 19, 2026Jan 19, 2026
    • Sparse csc and csr arrays backed by on-disk storage in Zarr or HDF5
      Jupyter Notebook
      0801Updated Jan 19, 2026Jan 19, 2026
    • Bring your single-cell data to life
      JavaScript
      1895152Updated Jan 19, 2026Jan 19, 2026
    • C++
      1200Updated Dec 6, 2025Dec 6, 2025
    • demuxEM

      Public
      Demultiplexing cell/nucleus hashing data for single-cell genomics
      Python
      4260Updated May 22, 2025May 22, 2025
    • nmf-torch

      Public
      Python
      61200Updated May 21, 2025May 21, 2025
    • Python
      106300Updated May 21, 2025May 21, 2025
    • UMI-tools

      Public
      Tools for handling Unique Molecular Identifiers in NGS data sets
      Python
      201000Updated Apr 16, 2025Apr 16, 2025
    • Test data and scripts for cumulus_feature_barcoding
      Shell
      0000Updated Feb 6, 2025Feb 6, 2025
    • Conda recipes for the bioconda channel.
      Shell
      3.8k000Updated Jun 13, 2024Jun 13, 2024
    • Data used for CI test of pegasus repo
      0000Updated Jan 7, 2024Jan 7, 2024
    • Python
      1020Updated Sep 13, 2022Sep 13, 2022
    • Jupyter Notebook
      33000Updated Apr 19, 2022Apr 19, 2022
    • Tutorial notebooks of Pegasus
      Jupyter Notebook
      0000Updated Apr 11, 2022Apr 11, 2022
    • Genomics Workflows on AWS
      Shell
      110000Updated Mar 20, 2022Mar 20, 2022
    • TRUST4

      Public
      TCR and BCR assembly from RNA-seq data
      C
      60000Updated Mar 17, 2022Mar 17, 2022
    • scCODA

      Public
      A statistical test for compositional changes in scRNA
      Jupyter Notebook
      27000Updated Mar 3, 2022Mar 3, 2022
    • 0000Updated Jan 10, 2022Jan 10, 2022
    • hnswlib

      Public
      Header-only C++/python library for fast approximate nearest neighbors
      C++
      783000Updated Oct 4, 2021Oct 4, 2021
    • 0000Updated Jul 16, 2021Jul 16, 2021
    • Dr. Bo Li's lab website
      HTML
      0000Updated Jan 6, 2021Jan 6, 2021
    • A place to submit conda recipes before they become fully fledged conda-forge feedstocks
      Python
      5.7k000Updated Dec 30, 2020Dec 30, 2020
    • A conda-smithy repository for louvain.
      6000Updated Dec 28, 2020Dec 28, 2020
    • Python
      0100Updated May 1, 2020May 1, 2020
    • R
      0000Updated Mar 6, 2020Mar 6, 2020