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@scverse

scverse

Foundational tools for omics data in the life sciences
README.md

Welcome to scverse!

scverse is a community that develops and maintains foundational tools for single-cell omics data analysis in primarily Python.

Here's how to get started:

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  1. scanpy scanpy Public

    Single-cell analysis in Python. Scales to >1M cells.

    Python 2k 612

  2. anndata anndata Public

    Annotated data.

    Python 599 157

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 224 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 84 19

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.3k 374

  6. scirpy scirpy Public

    A scanpy extension to analyse single-cell TCR and BCR data.

    Python 225 36

Repositories

Showing 10 of 52 repositories
  • scanpy Public

    Single-cell analysis in Python. Scales to >1M cells.

    scverse/scanpy’s past year of commit activity
    Python 1,988 BSD-3-Clause 612 490 (6 issues need help) 68 Updated Feb 5, 2025
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 43 BSD-3-Clause 15 68 5 Updated Feb 4, 2025
  • prelude-runner Public

    Jupyter notebook runner that executes preludes before each cell

    scverse/prelude-runner’s past year of commit activity
    Python 0 Apache-2.0 0 1 0 Updated Feb 4, 2025
  • scverse-tutorials Public

    Tutorials for learning scverse

    scverse/scverse-tutorials’s past year of commit activity
    Python 14 BSD-3-Clause 13 13 5 Updated Feb 4, 2025
  • governance Public

    Governance docs for scverse

    scverse/governance’s past year of commit activity
    7 BSD-3-Clause 0 19 2 Updated Feb 4, 2025
  • fast-array-utils Public

    Fast array utilities

    scverse/fast-array-utils’s past year of commit activity
    Python 2 MPL-2.0 0 3 1 Updated Feb 4, 2025
  • scanpy-tutorials Public

    Scanpy Tutorials.

    scverse/scanpy-tutorials’s past year of commit activity
    Jupyter Notebook 196 BSD-3-Clause 118 15 (1 issue needs help) 1 Updated Feb 4, 2025
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata’s past year of commit activity
    Python 249 BSD-3-Clause 47 190 6 Updated Feb 4, 2025
  • spatialdata-io Public
    scverse/spatialdata-io’s past year of commit activity
    Python 48 BSD-3-Clause 32 40 10 Updated Feb 4, 2025
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 68 11 18 4 Updated Feb 4, 2025
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