Help

mudata spatialdata scanpy For questions about using scanpy. anndata scvi-tools For questions about using scvi-tools. muon squidpy scirpy For questions about scirpy and single-cell T-cell and B-cell receptor analysis in general.

Topic		Replies	Views	Activity
About the Help category Help		0	532	March 4, 2022
[Usage clarification] Should the .obs in query and reference be exactly the same? scvi-tools		2	4	September 13, 2024
Trouble integrating my dataset into a reference dataset scvi-tools integration		5	17	September 13, 2024
How is the scArches scvi/scanvi pipeline different from the one on SCVI tutorials? scvi-tools scarches		0	3	September 13, 2024
Weird UMAP after running scVI scvi-tools		6	57	September 12, 2024
Split dotplot by condition scanpy		0	4	September 12, 2024
ZeroDivisionError using scvi-tools scvi-tools scatac-seq , scrna-seq		12	24	September 11, 2024
Trouble Making a Z-Score Heatmap scanpy		2	880	September 11, 2024
Macbook M1 M2 mps acceleration with scVI scvi-tools developer		7	1011	September 10, 2024
Embedding number for visualization scvi-tools integration , scvi		7	18	September 9, 2024
Loosing anndata .var layer when using sc.concat? scanpy		3	556	September 9, 2024
CNV scores in infercnvpy anndata		0	6	September 6, 2024
How to assess scanvi annoation transfer effect Help scanvi		1	12	September 6, 2024
Changing color/size of textfont with sc.pl.umap scanpy		2	29	September 4, 2024
What to do when the query dataset has different genes from the reference? scvi-tools		4	27	September 4, 2024
Anndata.concat([a,b], join="inner") does not behave as a.concat(b) anndata integration , anndata		1	96	September 4, 2024
scArches with multiple covariates scvi-tools scarches , integration , scvi		7	571	September 4, 2024
Scvi-tools and xenium scvi-tools scvi , integration		5	53	September 3, 2024
IndexError: list index out of range when running `sc.pp.neighbors(adata)` Help		4	12	September 3, 2024
Error in MrVI differential abundance scvi-tools		0	8	September 2, 2024
How to extract transformed polygons from sdata.shapes? spatialdata		3	14	September 2, 2024
ImportError: to_polygons Help		0	3	September 1, 2024
Can I use the package scib-metrics on methods that don't output an embedding? Help scrna-seq , integration		6	217	August 31, 2024
Autotune on custom model class scvi-tools		4	8	August 30, 2024
Doublet removal: solo model train error scvi-tools scvi		13	31	August 29, 2024
Understanding `differential_expression()` and lvm-DE scvi-tools		3	7	August 28, 2024
Pre-defined validation data scvi-tools scvi		1	11	August 27, 2024
How to compare different parameter sets using the validation loss? Help scvi , integration		6	353	August 26, 2024
Key error: 'coords' Help		0	9	August 26, 2024
SCVI and SCANVI for label transfer how to assess accuracy? scvi-tools scanvi		3	47	August 20, 2024