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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 807

  2. anndata anndata Public

    Annotated data.

    Python 783 220

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 483

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 612 128

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 408 55

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 354 69

Repositories

Showing 10 of 100 repositories
  • anndata-rs Public
    scverse/anndata-rs's past year of commit activity
    Rust 51 BSD-3-Clause 15 12 3 Updated Oct 28, 2026
  • benchmark Public

    Code for running benchmarks

    scverse/benchmark's past year of commit activity
    Rust 4 GPL-3.0 0 7 1 Updated Oct 28, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR's past year of commit activity
    R 201 24 50 10 Updated Oct 28, 2026
  • squidpy Public

    Spatial Single Cell Analysis in Python

    scverse/squidpy's past year of commit activity
    Python 612 BSD-3-Clause 128 83 (1 issue needs help) 26 Updated Oct 28, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 408 MIT 55 16 16 Updated Oct 28, 2026
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 14 BSD-3-Clause 0 37 1 Updated Oct 28, 2026
  • pytometry Public

    Flow & mass cytometry analytics.

    scverse/pytometry's past year of commit activity
    Python 61 Apache-2.0 15 13 (2 issues need help) 5 Updated Oct 28, 2026
  • pertpy Public

    Single-cell perturbation analysis

    scverse/pertpy's past year of commit activity
    Python 354 MIT 69 9 5 Updated Oct 28, 2026
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata's past year of commit activity
    Python 134 BSD-3-Clause 28 10 2 Updated Oct 28, 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 72 MIT 6 23 12 Updated Oct 28, 2026
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