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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 607

  2. anndata anndata Public

    Annotated data.

    Python 588 155

  3. muon muon Public

    muon is a multimodal omics Python framework

    Python 222 31

  4. mudata mudata Public

    Multimodal Data (.h5mu) implementation for Python

    Python 79 17

  5. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.3k 366

  6. scirpy scirpy Public

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

    Python 222 35

Repositories

Showing 10 of 51 repositories
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot’s past year of commit activity
    Python 38 BSD-3-Clause 14 64 8 Updated Dec 23, 2024
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools’s past year of commit activity
    Python 1,276 BSD-3-Clause 366 43 (1 issue needs help) 12 Updated Dec 23, 2024
  • scanpy Public

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

    scverse/scanpy’s past year of commit activity
    Python 1,957 BSD-3-Clause 607 507 (6 issues need help) 74 Updated Dec 20, 2024
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io’s past year of commit activity
    SCSS 1 6 17 2 Updated Dec 19, 2024
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR’s past year of commit activity
    R 64 11 21 5 Updated Dec 19, 2024
  • rapids_singlecell Public

    Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.

    scverse/rapids_singlecell’s past year of commit activity
    Python 157 MIT 23 15 3 Updated Dec 19, 2024
  • spatialdata-notebooks Public
    scverse/spatialdata-notebooks’s past year of commit activity
    Jupyter Notebook 39 BSD-3-Clause 19 6 5 Updated Dec 19, 2024
  • anndata Public

    Annotated data.

    scverse/anndata’s past year of commit activity
    Python 588 BSD-3-Clause 155 193 (4 issues need help) 54 Updated Dec 19, 2024
  • scvi-tutorials Public

    Notebooks used in scvi-tools tutorials

    scverse/scvi-tutorials’s past year of commit activity
    Jupyter Notebook 47 BSD-3-Clause 25 8 6 Updated Dec 19, 2024
  • rapids_singlecell-notebooks Public
    scverse/rapids_singlecell-notebooks’s past year of commit activity
    Jupyter Notebook 3 MIT 1 0 0 Updated Dec 19, 2024
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