If you’d like to see your tool included here, please open a pull request!

With ecosystem, we mean the broader single-cell related tools that operate on AnnData. If your tool doesn’t do this, but is useful for analysing single cell data we also accept light wrappers for some tools in scanpy.external.


Interactive manifold viewers.


RNA velocity

Fate mapping

  • CellRank Helmholtz Munich

    CellRank is a toolkit to uncover cellular dynamics based on scRNA-seq data with RNA velocity annotation by detecting initial and terminal populations, inferring fate potentials and uncovering gene expression trends towards specific terminal populations.

Differential expression

Data integration

Modeling perturbations


  • scvi-tools Berkeley

    scvi-tools hosts deep generative models (DGM) for end-to-end analysis of single-cell omics data (e.g., scVI, scANVI, totalVI). It also contains several primitives to build novel DGMs.

Adaptive immune receptor repertoire (AIRR)

  • scirpy Medical University of Innsbruck

    scirpy is a scanpy extension to expore single-cell T-cell receptor (TCR) and B-cell receptor (BCR) repertoires.
  • dandelion University of Cambridge

    dandelion is a single-cell BCR-seq network analysis package that integrates with transcriptomic data analyzed via scanpy.

Feature selection

  • triku 🦔 Biodonostia Health Research Institute

Annotation/ Enrichment Analysis

Analyses using curated prior knowledge

  • dorothea for Transcription Factor activities Institute for Computational Biomedicine, Heidelberg University

  • progeny for footprint-based pathway activities Institute for Computational Biomedicine, Heidelberg University

  • Cubé Harvard University

    Intuitive Nonparametric Gene Network Search Algorithm that learns from existing biological pathways & multiplicative gene interference patterns.

Spatial Transcriptomics Tools

  • PASTE Princeton

    PASTE is a computational method to align and integrate spatial transcriptomics data across adjacent tissue slices by leveraging both gene expression similarity and spatial distances between spots.