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Research · Topic

Open-source software

Tools whose code is public, documented and maintained for others to use.

2 people10 publications11 toolsAlso called open-source, python, scverse

Research themes

1

People

1

Alumni

1

Open positions

1

Software

11

  • scVelo

    RNA velocity generalized through dynamical modeling.

    515v0.3.49 mo agoPython

  • scib

    Benchmarking analysis of data integration tools.

    436v1.2.16 mo agoPython

  • scArches

    Reference mapping for single-cell genomics.

    414v0.5.13 y agoJupyter Notebook

  • Scanpy

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

    2.6K1.12.58 d agoPython

  • anndata

    Annotated data.

    7830.13.449 d agoPython

  • ehrapy

    Electronic Health Record Analysis with Python.

    370v0.16.04 d agoPython

  • scGen

    Single cell perturbation prediction.

    361v2.1.05 y agoPython

  • moscot

    Multi-omic single-cell optimal transport tools.

    219v0.5.22 mo agoPython

  • CPA

    The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level.

    157v0.5.03 y agoPython

  • DRVI

    Unsupervised Deep Disentangled Representation of Single-Cell Omics

    83v0.2.823 d agoPython

On the map

10

Plate II

Pl. II The map of publications (Plate II) with the 10 works tagged open-source software drawn large in the colour of their island.

10 of 742 works marked · data synced 6 Nov 2026

Publications

10

  1. Spatial, Omics Data
  2. Independent Component, Graph
  3. Images, Deep Learning
  4. Representations, Single Cell
  5. Spatial, Omics Data
  6. Cell Atlas, Integration
  7. Cell Atlas, Integration
  8. Single Cell RNA, Gene Expression
  9. Representations, Single Cell
  10. Single Cell RNA, Gene Expression

News

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