Open neuromusic opened 5 years ago
for context on how scanpy visualizes this data ...
import scanpy as sc
pbmc = sc.datasets.pbmc68k_reduced()
sc.tl.rank_genes_groups(
pbmc,
groupby='louvain'
)
sc.pl.rank_genes_groups(pbmc)
I love this and think we should do it. I'll noodle.
The AnnData formalism for differential expression is more general than just scanpy algorithms. @vals said it would be helpful if cellxgene could bring in these kinds of data, since he can store his scVI differential expression results in this form.
Also relevant for chanzuckerberg/single-cell#15 -- this kind of data could be brought in via gene sets.
As a scanpy user who has already computed differential expression via
scanpy.tl.rank_genes_groups
and saved the results to.uns['rank_genes_groups'
], I want to view these results in cellxgene so that I can explore marker genes that differentiate labeled groups of cells.See: https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.rank_genes_groups.html