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Category Topics
HELP

For help with a particular scverse package
scvi-tools scanpy squidpy scirpy anndata muon mudata
407

GENERAL

Use this for topics broader in scope than one particular package.
scRNA-seq scATAC-seq CITE-seq Multiome Visium
39

ANNOUNCEMENTS

For scverse-related announcements.
3

ECOSYSTEM

For help with ecosystem packages
cell2location scVelo cellrank scArches
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1


Latest

Welcome to the scverse discourse!
Announcements
3
Dec '20
What is the best way to extract a “full” batch effect corrected count matrix
from scVI model?
scvi-tools
scvi
2
2h
No unique function for adata.obs
scanpy
scvi
1
9h
Regressing out variables in pearson residual normalization
scanpy
1
13h
Random umap and clustering resullt
scanpy
5
13h
Got 0 probability for pvals_adj. What mean is this?
General
0
1d
scRNA data integration
General
integration
0
1d
Trouble Reading .h5 files
scanpy
0
1d
Hyperparameter optimization of SCVI model using the autotune package
scvi-tools
4
1d
“ValueError: cannot specify integer `bins` when input data contains infinity” in
multi sample data
scanpy
integration multivi
5
2d
Better input data for finding DEGs
scanpy
0
3d
Finding markers (DEGs) methods
scanpy
0
3d
UserWarning: No data for colormapping provided via ‘c’. Parameters ‘cmap’ will
be ignored
scanpy
scvi developer
6
3d
Scverse community meetings
Announcements
3
5d
How to get [“label”, “centroid”] for each cell with cellpose
squidpy
1
5d
Pseudobulk DE gene Analysis in scverse ecosystem
scRNA-seq
10
8d
How to check average gene expression for each of 2 conditions within a cluster
in scanpy?
Help
0
9d
Plotting repertoire overlap as a heatmap with scirpy
scirpy
plotting
2
9d
Squidpy comparative statistics
squidpy
2
11d
Centrality Score: Understanding average clustering
squidpy
1
11d
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