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@czbiohub-sf

Chan Zuckerberg Biohub San Francisco

CZ Biohub SF logo

The Chan Zuckerberg Biohub San Francisco is a nonprofit research institute focused on understanding the underlying mechanisms of disease and on developing new technologies that will lead to actionable diagnostics and effective therapies. We are a regional research endeavor with international reach, where the San Francisco Bay Area’s leading academic institutions (Stanford University; University of California, Berkeley; and University California, San Francisco) join forces with CZ Biohub’s innovative internal team to catalyze impact, spurring partnerships that benefit people around the world. The tools and technologies we create will always be freely available to scientists everywhere.

Affiliated GitHub organizations

The following GitHub organizations are also part of CZ Biohub San Francisco's GitHub presence:

Contact us!

We welcome comments, questions, and inquiries. Please usethis form to contact us.

Interested in working with us? Search our job openingshere.

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  1. noise2selfnoise2selfPublic

    A framework for blind denoising with self-supervision.

    Jupyter Notebook 343 76

  2. tabula-muristabula-murisPublic

    Code and annotations for the Tabula Muris single-cell transcriptomic dataset.

    HTML 190 95

  3. xicorxicorPublic archive

    xi correlation method adapted for python

    Jupyter Notebook 149 17

  4. tabula-muris-senistabula-muris-senisPublic

    Tabula Muris Senis

    Jupyter Notebook 100 26

  5. tabula-sapienstabula-sapiensPublic

    Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens

    Jupyter Notebook 41 9

  6. zebrahub_analysiszebrahub_analysisPublic

    Analysis of single-cell single-embryo RNA seq data from the zebrafish developmental atlas Zebrahub.

    Jupyter Notebook 5 1

Repositories

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Showing 10 of 109 repositories
  • ulc-malaria-scope Public

    Instrument control software for the Remoscope project.

    czbiohub-sf/ulc-malaria-scope’s past year of commit activity
    Python 10 1 0 UpdatedMar 18, 2025
  • biahub Public

    HUB for Bio Image Analysis

    czbiohub-sf/biahub’s past year of commit activity
    Python0BSD-3-Clause0 16 9 UpdatedMar 18, 2025
  • zebrahub-multiome-analysis Public

    A repository for scripts and notebooks to process and analyze single-cell Multiome datasets from early zebrafish embryos (zebrahub)

    czbiohub-sf/zebrahub-multiome-analysis’s past year of commit activity
    Jupyter Notebook 2BSD-3-Clause 1 0 0 UpdatedMar 17, 2025
  • napari-iohub Public

    OME-Zarr viewer for napari with iohub as the I/O backend

    czbiohub-sf/napari-iohub’s past year of commit activity
    Python 3BSD-3-Clause0 9 2 UpdatedMar 17, 2025
  • iohub Public

    Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata

    czbiohub-sf/iohub’s past year of commit activity
    Python 34BSD-3-Clause 7 36(1 issue needs help) 9 UpdatedMar 12, 2025
  • subcellular-proteomics-curation Public Forked frommffrank/subcellular-proteomics-curation

    Code and documentation for the curation of proteinxlocation datasets

    czbiohub-sf/subcellular-proteomics-curation’s past year of commit activity
    Python0MIT 26 0 1 UpdatedMar 12, 2025
  • compmicro-ndutils-env Public

    Shared ndutils environment for maintained by the CompMicro platform

    czbiohub-sf/compmicro-ndutils-env’s past year of commit activity
    Dockerfile0BSD-3-Clause0 1 0 UpdatedMar 7, 2025
  • reglo-icc-pump-control Public

    Python communication driver for Masterflex Ismatec Reglo ICC programmable peristaltic pumps

    czbiohub-sf/reglo-icc-pump-control’s past year of commit activity
    Python 1BSD-3-Clause0 0 0 UpdatedMar 6, 2025
  • shrimPy Public

    shrimPy: Smart High-throughput Robust Imaging & Measurement in Python

    czbiohub-sf/shrimPy’s past year of commit activity
    Python 8BSD-3-Clause 2 30 2 UpdatedMar 6, 2025
  • proteinxlocation Public Forked fromchanzuckerberg/cellxgene

    An interactive explorer for single-cell transcriptomics data

    czbiohub-sf/proteinxlocation’s past year of commit activity
    JavaScript0MIT 131 0 0 UpdatedFeb 28, 2025

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