Ecosystem

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.

Viewers

Interactive manifold viewers.

Portals

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

  • 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