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@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:

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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 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
  • rapids-singlecell Public

    rapids-singlecell: GPU-accelerated framework for scRNA analysis

    scverse/rapids-singlecell's past year of commit activity
    Python 409 MIT 55 14 13 Updated Nov 8, 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 Nov 8, 2026
  • scverse-doc Public

    scverse doc theme & utilities

    scverse/scverse-doc's past year of commit activity
    Python 2 MPL-2.0 0 3 0 Updated Nov 8, 2026
  • scanpy Public

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

    scverse/scanpy's past year of commit activity
    Python 2,610 BSD-3-Clause 808 440 (3 issues need help) 103 Updated Nov 8, 2026
  • gget Public

    🧬 gget enables efficient querying of genomic reference databases

    scverse/gget's past year of commit activity
    Python 1,212 BSD-2-Clause 99 25 5 Updated Nov 8, 2026
  • zarr-convention-dataframe Public

    A zarr convention for dataframes

    scverse/zarr-convention-dataframe's past year of commit activity
    3 MIT 1 1 1 Updated Nov 8, 2026
  • PyDESeq2 Public

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

    scverse/PyDESeq2's past year of commit activity
    Python 769 MIT 95 42 23 Updated Nov 8, 2026
  • anndataR Public

    AnnData interoperability in R

    scverse/anndataR's past year of commit activity
    R 201 24 49 11 Updated Nov 7, 2026
  • scverse.github.io Public

    scverse.org website

    scverse/scverse.github.io's past year of commit activity
    SCSS 4 MPL-2.0 11 5 2 Updated Nov 7, 2026
  • gatac Public

    GPU-accelerated scATACseq analysis

    scverse/gatac's past year of commit activity
    Python 3 BSD-3-Clause 0 0 0 Updated Nov 6, 2026
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