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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 783 222

  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 409 55

  6. pertpy pertpy Public

    Single-cell perturbation analysis

    Python 357 70

Repositories

Showing 10 of 107 repositories
  • anndata Public

    Annotated data.

    scverse/anndata's past year of commit activity
    Python 783 BSD-3-Clause 222 194 (4 issues need help) 94 Updated Nov 6, 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 10 Updated Nov 6, 2026
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    scverse/gget's past year of commit activity
    Python 1,211 BSD-2-Clause 99 25 5 Updated Nov 5, 2026
  • gatac Public

    GPU-accelerated scATACseq analysis

    scverse/gatac's past year of commit activity
    Python 3 BSD-3-Clause 0 0 1 Updated Nov 5, 2026
  • fast-array-utils Public

    Fast array utilities

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

    Analysis framework for morphological profiling data

    scverse/mantispy's past year of commit activity
    Python 15 BSD-3-Clause 1 61 5 Updated Nov 5, 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 3 Updated Nov 5, 2026
  • scvi-tools Public

    Deep probabilistic analysis of single-cell and spatial omics data

    scverse/scvi-tools's past year of commit activity
    Python 1,720 BSD-3-Clause 483 12 (1 issue needs help) 13 Updated Nov 5, 2026
  • scanpy Public

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

    scverse/scanpy's past year of commit activity
    Python 2,609 BSD-3-Clause 808 440 (3 issues need help) 95 Updated Nov 5, 2026
  • spatialdata-spec Public

    Specification for the SpatialData format

    scverse/spatialdata-spec's past year of commit activity
    2 0 2 4 Updated Nov 5, 2026
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