With ecosystem, we mean single-cell related tools that operate on AnnData. Here, we list some that do not have an interface in the external API.


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.

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