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.

• cellxgene via direct reading of .h5ad CZI

• cirrocumulus via direct reading of .h5ad Broad Inst.

• cell browser via exporing through cellbrowser() UCSC

• SPRING via exporting through spring_project() Harvard Med

Portals

• the Gene Expression Analysis Resource U Maryland

• the Galaxy Project for the Human Cell Atlas [tweet] U Freiburg

• the Expression Atlas EMBL-EBI

RNA velocity

• scVelo Helmholtz Munich

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

• diffxpy Helmholtz Munich

Data integration

• scanaroma MIT

Modeling perturbations

• scGen / trVAE Helmholtz Munich

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