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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 341 72

  2. tabula-muris tabula-muris Public

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

    HTML 188 91

  3. xicor xicor Public archive

    xi correlation method adapted for python

    Jupyter Notebook 147 17

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

    Tabula Muris Senis

    Jupyter Notebook 100 26

  5. tabula-sapiens tabula-sapiens Public

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

    Jupyter Notebook 40 8

  6. zebrahub_analysis zebrahub_analysis Public

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

    Jupyter Notebook 4 1

Repositories

Showing 10 of 99 repositories
  • 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 3 BSD-3-Clause 0 8 1 Updated Dec 25, 2024
  • DeepGenotype Public

    Calculate the outcome genotype frequencies in CRISPR genome editing experiments using deep sequencing reads.

    czbiohub-sf/DeepGenotype’s past year of commit activity
    HTML 1 BSD-3-Clause 0 0 0 Updated Dec 24, 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 32 BSD-3-Clause 8 32 (2 issues need help) 6 Updated Dec 20, 2024
  • ulc-malaria-autofocus Public

    A single-shot autofocus CNN for the Remoscope project

    czbiohub-sf/ulc-malaria-autofocus’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Dec 19, 2024
  • remo-stats-utils Public

    This is a collection of statistics utilities used to support the Remoscope project at the Chan Zuckerberg Biohub San Francisco.

    czbiohub-sf/remo-stats-utils’s past year of commit activity
    Python 0 BSD-3-Clause 0 0 0 Updated Dec 18, 2024
  • lfm-data-utilities Public

    A collection of auxiliary data processing tools used in the Remoscope project.

    czbiohub-sf/lfm-data-utilities’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 0 0 Updated Dec 18, 2024
  • shrimPy Public

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

    czbiohub-sf/shrimPy’s past year of commit activity
    Python 8 BSD-3-Clause 1 30 2 Updated Dec 17, 2024
  • czb-ui Public

    CZ Biohub's higher level components made with CZI's Science Design System Component Library.

    czbiohub-sf/czb-ui’s past year of commit activity
    TypeScript 5 BSD-3-Clause 0 12 1 Updated Dec 17, 2024
  • proteinxlocation Public Forked from chanzuckerberg/cellxgene

    An interactive explorer for single-cell transcriptomics data

    czbiohub-sf/proteinxlocation’s past year of commit activity
    JavaScript 0 MIT 122 0 1 Updated Dec 12, 2024
  • 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 2 BSD-3-Clause 1 1 0 Updated Dec 10, 2024

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