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
CZIcirrocumulus via direct reading of
.h5ad
Broad Inst.cell browser via exporing through
cellbrowser()
UCSCSPRING 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
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.
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.