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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 778

  2. anndata anndata Public

    Annotated data.

    Python 772 209

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 474

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 598 121

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 394 52

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 344 66

Repositories

Showing 10 of 97 repositories
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 8 BSD-3-Clause 0 33 4 Updated Sep 18, 2026
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    scverse/gget's past year of commit activity
    Python 1,199 BSD-2-Clause 97 25 19 Updated Sep 18, 2026
  • fast-array-utils Public

    Fast array utilities

    scverse/fast-array-utils's past year of commit activity
    Python 15 MPL-2.0 5 17 (1 issue needs help) 6 Updated Sep 17, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR's past year of commit activity
    R 196 22 40 12 Updated Sep 17, 2026
  • liana Public

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

    scverse/liana's past year of commit activity
    Python 315 BSD-3-Clause 37 10 3 Updated Sep 17, 2026
  • acumen Public
    scverse/acumen's past year of commit activity
    Python 8 MIT 1 1 2 Updated Sep 17, 2026
  • annbatch Public

    Minibatch loading for on-disk anndata files, co-developed by Lamin Labs and scverse

    scverse/annbatch's past year of commit activity
    Python 68 MIT 6 24 11 Updated Sep 17, 2026
  • anndata-rs Public
    scverse/anndata-rs's past year of commit activity
    Rust 50 17 12 10 Updated Sep 17, 2026
  • scverse-io Public

    Read various formats into AnnData and MuData

    scverse/scverse-io's past year of commit activity
    3 BSD-3-Clause 0 11 0 Updated Sep 17, 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 2 0 6 Updated Sep 17, 2026
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