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scverse

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

Welcome to scverse®!

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 >100M cells.

    Python 2.6k 808

  2. anndata anndata Public

    Annotated data.

    Python 784 221

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 481

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 613 128

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 409 56

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 355 69

Repositories

Showing 10 of 106 repositories
  • anndata Public

    Annotated data.

    scverse/anndata's past year of commit activity
    Python 784 BSD-3-Clause 221 193 (4 issues need help) 91 Updated Nov 1, 2026
  • scvi-tools-site Public

    Website of scVI-Tools: Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools-site's past year of commit activity
    JavaScript 0 BSD-3-Clause 2 0 0 Updated Nov 1, 2026
  • repo-health Public

    Automated checks for security and consistency on scverse.org github repositories

    scverse/repo-health's past year of commit activity
    Python 1 MPL-2.0 0 3 4 Updated Nov 1, 2026
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    scverse/gget's past year of commit activity
    Python 1,210 BSD-2-Clause 98 25 4 Updated Nov 1, 2026
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 14 BSD-3-Clause 0 41 0 Updated Nov 1, 2026
  • PyDESeq2 Public

    A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

    scverse/PyDESeq2's past year of commit activity
    Python 768 MIT 94 41 19 Updated Nov 1, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 409 MIT 56 13 13 Updated Oct 31, 2026
  • gatac Public

    GPU-accelerated scATACseq analysis

    scverse/gatac's past year of commit activity
    Python 3 BSD-3-Clause 0 0 0 Updated Oct 31, 2026
  • liana Public

    LIANA+: an all-in-one framework for cell-cell communication

    scverse/liana's past year of commit activity
    Python 325 BSD-3-Clause 39 8 1 Updated Oct 31, 2026
  • liana-tutorials Public
    scverse/liana-tutorials's past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 0 0 0 Updated Oct 31, 2026
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