Help

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

Topic		Replies	Views	Activity
About the Help category Help		0	556	March 4, 2022
Modify gene identifiers stored in existing scVI model scvi-tools		1	11	April 20, 2025
Anndata Manager Store scvi-tools		11	25	April 20, 2025
Scvi package can't be installed into google colab? scvi-tools scvi		6	12	April 20, 2025
How to retreive the V,D,J gene segment idenifiers and CD3 sequence give a clone_id? scirpy		1	5	April 18, 2025
Workflow advice for totalVI in CITE-seq Multiplexed data scvi-tools totalvi		1	6	April 17, 2025
Is the scVI model applicable to bulk RNA-seq data from cell lines? scvi-tools scvi		1	9	April 16, 2025
Unexpected DE test results in scvi version 1.3.0 (as compared with version 1.1.2) scvi-tools		5	34	April 16, 2025
Problems with Bayes factors and LFC changes using model.differential_expression() scvi-tools diff-exp		2	24	April 14, 2025
Memory Usage in multiple New Formats anndata		0	13	April 13, 2025
Best Practices for Multi-Panel Figures scanpy plotting		0	13	April 11, 2025
Unexplained change in UMAP scanpy		0	15	April 11, 2025
Lazy Loading Anndata backed in Zarr Arrays from Disk anndata		4	42	April 11, 2025
How to transfer annotation from cell subset to original object? anndata		1	26	April 10, 2025
How to plot annotation in Xenium data using spatialdata spatialdata		8	68	April 10, 2025
How should I calculate the knn entropy using the leiden clusters? Help integration , scvi		1	13	April 10, 2025
Understanding scVI integration inside R with Seurat v5 & SCTransform scvi-tools integration		1	48	April 6, 2025
How to fix number of nodes used in HPC environment with scvi.train (via R & reticulate)? scvi-tools integration		8	34	April 10, 2025
Stacked violin API related question scanpy		2	349	April 1, 2025
Any MLX (MPS) framework accelerate solution for scanpy？ scanpy		1	40	March 31, 2025
How to filter out specific cell types in spatialdata similar to anndata? spatialdata		0	22	March 27, 2025
Getting the same values to have the same colors across multiple plots of spatial_segment? squidpy		0	8	March 24, 2025
inferCNVpy after running scVI with batch as key Help integration , scvi		5	716	March 24, 2025
Suggestions for training on xenium spatial transcriptomics dataset scvi-tools		5	119	March 22, 2025
How to generate continuous colormap to plot the (co-)expression of multiple genes Help		0	13	March 20, 2025
Error when running scvi.data.add_dna_sequence scvi-tools scvi , integration		1	36	March 18, 2025
Scvi-tools solo return synthetic doublets scvi-tools		3	22	March 18, 2025
SysVI model and normalized expression scvi-tools scvi , integration		1	47	March 15, 2025
Scvi-tools and xenium scvi-tools scvi , integration		7	304	March 13, 2025
Unexpected exception formatting exception when prepare_query_anndata scvi-tools scanvi		4	41	March 11, 2025