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    39 repositories

    • cumulus

      Public
      Cloud-based scalable and efficient single-cell genomics workflows
      WDL
      •
      BSD 3-Clause "New" or "Revised" License
      •36•68•12•0•Updated Feb 17, 2026Feb 17, 2026

    • stratocumulus

      Public
      Backend component of Cumulus for different cloud environments.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•1•1•Updated Feb 16, 2026Feb 16, 2026

    • lilab-bcb.github.io

      Public
      Website of Dr Li's Lab
      HTML
      •0•0•0•0•Updated Feb 12, 2026Feb 12, 2026

    • pegasus

      Public
      A tool for analyzing trascriptomes of millions of single cells.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •25•93•12•2•Updated Jan 23, 2026Jan 23, 2026

    • pegasusio

      Public
      pegasus io module for reading/writing single-cell genomics data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•8•1•1•Updated Jan 22, 2026Jan 22, 2026

    • altocumulus

      Public
      Command line tool for submitting WDL jobs to Terra or Cromwell server.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•7•3•1•Updated Jan 19, 2026Jan 19, 2026

    • backedarray

      Public
      Sparse csc and csr arrays backed by on-disk storage in Zarr or HDF5
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•8•0•1•Updated Jan 19, 2026Jan 19, 2026

    • cirrocumulus

      Public
      Bring your single-cell data to life
      visualizationwebglbioinformaticsspatialdata-visualizationscrna-seqtranscriptomicssingle-cell10xsmartseq2
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •18•95•15•2•Updated Jan 19, 2026Jan 19, 2026

    • cumulus_feature_barcoding

      Public
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Dec 6, 2025Dec 6, 2025

    • demuxEM

      Public
      Demultiplexing cell/nucleus hashing data for single-cell genomics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•2•6•0•Updated May 22, 2025May 22, 2025

    • nmf-torch

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•12•0•0•Updated May 21, 2025May 21, 2025

    • harmony-pytorch

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•63•0•0•Updated May 21, 2025May 21, 2025

    • UMI-tools

      Public
      Tools for handling Unique Molecular Identifiers in NGS data sets
      Python
      •
      MIT License
      •201•0•0•0•Updated Apr 16, 2025Apr 16, 2025

    • cumulus-fb-test

      Public
      Test data and scripts for cumulus_feature_barcoding
      Shell
      •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •
      MIT License
      •3.8k•0•0•0•Updated Jun 13, 2024Jun 13, 2024

    • pegasus-test-data

      Public
      Data used for CI test of pegasus repo
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jan 7, 2024Jan 7, 2024

    • cirrocumulus-app-engine

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•2•0•Updated Sep 13, 2022Sep 13, 2022

    • terra-docker

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •33•0•0•0•Updated Apr 19, 2022Apr 19, 2022

    • pegasus-tutorials

      Public
      Tutorial notebooks of Pegasus
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 11, 2022Apr 11, 2022

    • aws-genomics-workflows

      Public
      Genomics Workflows on AWS
      Shell
      •
      MIT No Attribution
      •110•0•0•0•Updated Mar 20, 2022Mar 20, 2022

    • TRUST4

      Public
      TCR and BCR assembly from RNA-seq data
      C
      •
      GNU General Public License v3.0
      •60•0•0•0•Updated Mar 17, 2022Mar 17, 2022

    • scCODA

      Public
      A statistical test for compositional changes in scRNA
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •27•0•0•0•Updated Mar 3, 2022Mar 3, 2022

    • merge-test

      Public
      0•0•0•0•Updated Jan 10, 2022Jan 10, 2022

    • hnswlib

      Public
      Header-only C++/python library for fast approximate nearest neighbors
      C++
      •
      Apache License 2.0
      •783•0•0•0•Updated Oct 4, 2021Oct 4, 2021

    • pegasusio-test-data

      Public
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 16, 2021Jul 16, 2021

    • lilab-website-old

      Public
      Dr. Bo Li's lab website
      HTML
      •0•0•0•0•Updated Jan 6, 2021Jan 6, 2021

    • staged-recipes

      Public
      A place to submit conda recipes before they become fully fledged conda-forge feedstocks
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5.7k•0•0•0•Updated Dec 30, 2020Dec 30, 2020

    • louvain-feedstock

      Public
      A conda-smithy repository for louvain.
      BSD 3-Clause "New" or "Revised" License
      •6•0•0•0•Updated Dec 28, 2020Dec 28, 2020

    • cumulus-experiment

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated May 1, 2020May 1, 2020

    • bcb-dockers

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Mar 6, 2020Mar 6, 2020