With ecosystem, we mean single-cell related tools that operate on :class:`~anndata.AnnData`. Here, we list some that do not have an interface in the :doc:`external API <external/index>`.
Interactive manifold viewers.
- cellxgene via direct reading of .h5ad CZI
- cirrocumulus via direct reading of .h5ad Broad Inst.
- cell browser via exporing through :func:`~scanpy.external.exporting.cellbrowser` UCSC
- SPRING via exporting through :func:`~scanpy.external.exporting.spring_project` Harvard Med
- the Gene Expression Analysis Resource U Maryland
- the Galaxy Project for the Human Cell Atlas [tweet] U Freiburg
- the Expression Atlas EMBL-EBI
- scVelo Helmholtz Munich
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.
- diffxpy Helmholtz Munich
- scanaroma MIT
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.
scirpy Medical University of Innsbruck
scirpy is a scanpy extension to expore single-cell T-cell receptor (TCR) and B-cell receptor (BCR) repertoires.