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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:

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

Interested in working with us? Search our job openings here.

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  1. noise2self noise2self Public

    A framework for blind denoising with self-supervision.

    Jupyter Notebook 329 69

  2. tabula-muris tabula-muris Public

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

    HTML 185 90

  3. xicor xicor Public archive

    xi correlation method adapted for python

    Jupyter Notebook 143 17

  4. tabula-muris-senis tabula-muris-senis Public

    Tabula Muris Senis

    Jupyter Notebook 93 26

  5. tabula-sapiens tabula-sapiens Public

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

    Jupyter Notebook 38 7

  6. zebrahub_analysis zebrahub_analysis Public

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

    Jupyter Notebook 2 1

Repositories

Showing 10 of 92 repositories
  • shrimPy Public

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

    czbiohub-sf/shrimPy’s past year of commit activity
    Python 7 BSD-3-Clause 1 33 5 Updated Sep 18, 2024
  • 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 29 BSD-3-Clause 6 25 (2 issues need help) 10 Updated Sep 17, 2024
  • 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 1 BSD-3-Clause 0 4 1 Updated Sep 13, 2024
  • zebrahub_analysis Public

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

    czbiohub-sf/zebrahub_analysis’s past year of commit activity
    Jupyter Notebook 2 1 1 1 Updated Sep 11, 2024
  • Rapid-QC-MS Public

    Realtime quality control for mass spectrometry data acquisition

    czbiohub-sf/Rapid-QC-MS’s past year of commit activity
    Python 13 2 15 1 Updated Sep 10, 2024
  • 2021-opencell-figures Public

    Public read-only repo for code and data related to the 2021 OpenCell preprint

    czbiohub-sf/2021-opencell-figures’s past year of commit activity
    Jupyter Notebook 4 1 2 0 Updated Sep 10, 2024
  • random-walk-epidemic-model Public

    A random walk epidemic model.

    czbiohub-sf/random-walk-epidemic-model’s past year of commit activity
    Jupyter Notebook 0 1 0 0 Updated Sep 10, 2024
  • sc2-guide-InSilicoSCR Public

    InSilico off-target screening for SC2 guides.

    czbiohub-sf/sc2-guide-InSilicoSCR’s past year of commit activity
    Python 0 0 0 0 Updated Sep 10, 2024
  • czbiohub-sf/covid19-transcriptomics-pathogenesis-diagnostics-results’s past year of commit activity
    Jupyter Notebook 5 7 0 0 Updated Sep 10, 2024
  • EpiGen-COVID19 Public

    Using both phylogenetic and time-series data from the COVID19 pandemic to estimate number of missing infections and predict forward epidemic trajectory.

    czbiohub-sf/EpiGen-COVID19’s past year of commit activity
    R 4 1 0 0 Updated Sep 10, 2024