Scanpy

[Diane Trout <diane@ghic.org>]

Hello,

(edited into a different thread since it's about a different package)


> > Which is a dependency for scanpy
> > https://pypi.org/project/scanpy/
> > 
> > Which is a single-cell RNA seq analysis package.
> 
> We probably want this!

:) It looked pretty useful and I noticed some of our collaborators were
also using it.

Scanpy takes advantage of a bunch of tools of various difficulties
to package.

anndata https://github.com/theislab/anndata
(packaged, need to create salsa project and file ITP)

umap-learn https://github.com/lmcinnes/umap
(packaged, need to create salsa project and file ITP)

MulticoreTSNE https://github.com/DmitryUlyanov/Multicore-TSNE
(Lacks release tags, haven't tried to package yet)

leidenalg https://github.com/vtraag/leidenalg
(partially packaged, need to fix boilerplate and add copyright)

louvain
https://github.com/vtraag/louvain-igraph
(partially packaged, need to fix boilerplate and add copyright
also upstream deprecated in favor of leidenalg, though scanpy &
monocle3 still use)

Cellbrowser
https://github.com/maximilianh/cellBrowser/blob/master/LICENSE
(Partially packaged, but so much embedded javascript :(  )

Diane