Skip to content
@scverse

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:

Pinned Loading

  1. scanpy scanpy Public

    Single-cell analysis in Python. Scales to >100M cells.

    Python 2.6k 797

  2. anndata anndata Public

    Annotated data.

    Python 780 220

  3. scvi-tools scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    Python 1.7k 480

  4. squidpy squidpy Public

    Spatial Single Cell Analysis in Python

    Python 608 124

  5. rapids-singlecell rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    Python 402 54

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 351 68

Repositories

Showing 10 of 97 repositories
  • anndata Public

    Annotated data.

    scverse/anndata's past year of commit activity
    Python 780 BSD-3-Clause 220 187 (4 issues need help) 92 Updated Oct 16, 2026
  • mantispy Public

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 12 BSD-3-Clause 0 37 1 Updated Oct 16, 2026
  • spatialdata Public

    An open and interoperable data framework for spatial omics data

    scverse/spatialdata's past year of commit activity
    Python 402 BSD-3-Clause 101 312 29 Updated Oct 16, 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) 5 Updated Oct 16, 2026
  • spatialdata-plot Public

    Static plotting for spatialdata

    scverse/spatialdata-plot's past year of commit activity
    Python 87 BSD-3-Clause 22 17 4 Updated Oct 16, 2026
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 402 MIT 54 13 14 Updated Oct 16, 2026
  • mudata Public

    Multimodal Data (.h5mu) implementation for Python

    scverse/mudata's past year of commit activity
    Python 134 BSD-3-Clause 28 11 4 Updated Oct 16, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 4 1 Updated Oct 16, 2026
  • spatialdata-io Public
    scverse/spatialdata-io's past year of commit activity
    Python 105 BSD-3-Clause 64 70 14 Updated Oct 16, 2026
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    scverse/gget's past year of commit activity
    Python 1,208 BSD-2-Clause 99 25 3 Updated Oct 15, 2026
View all repositories