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

• 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

Differential expression

• diffxpy Helmholtz Munich

Data integration

• scVI, see comparison Berkeley

• scanaroma MIT

Modeling perturbations

• scGen / trVAE Helmholtz Munich