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

Topic		Replies	Views	Activity
About the Help category Help		0	541	March 4, 2022
How to appropriately transfer annotations from anndata to seurat scvi-tools anndata		2	3	January 24, 2025
Best practice for handling custom points during SCVI training scvi-tools		4	29	January 24, 2025
Lazy loading of Zarr from S3 anndata		2	10	January 23, 2025
Any MLX (MPS) framework accelerate solution for scanpy？ scanpy		0	5	January 23, 2025
Integrating TRUST4 outputs into anndata GEX scirpy		3	19	January 22, 2025
Cell hashing analysis using muon muon		0	6	January 21, 2025
Workflow to integrate dataset from two different species scvi-tools		1	25	January 21, 2025
Scvi embedding from Census API by CellxGene scvi-tools		1	10	January 20, 2025
Dealing with multiple samples spatialdata		8	457	January 20, 2025
Cropping spatialdata to extent of shapes spatialdata		2	10	January 20, 2025
How to convert R matrix to anndata Help anndata , scvi		4	35	January 17, 2025
Using squidpy following scRNAseq and spatialRNASeq integration with scanorama and scanpy Help		0	12	January 17, 2025
Model cannot be initialized and return error scvi-tools		6	42	January 15, 2025
Error loading someone else's SCVI model: no such file (attr.pkl) scvi-tools scvi		1	14	January 13, 2025
Impact of batch on TotalVI results scvi-tools totalvi		1	35	January 5, 2025
Differential expression analysis scvi-tools		4	607	January 5, 2025
Napari_spatialdata colouring cell_labels and plotting specific transcripts spatialdata		3	179	December 28, 2024
What training datasets are used in the scVI pretrained model (version 2024-07-01)? scvi-tools integration , scvi		2	39	December 23, 2024
Suggestions for training on xenium spatial transcriptomics dataset scvi-tools		0	31	December 21, 2024
Issue with model.train() in scVI - Training Stuck at 0% scvi-tools scvi		1	31	December 15, 2024
Replicating data analysis using published pipeline scanpy		0	20	December 10, 2024
Train scVI on a sampled dataset scvi-tools		8	71	December 6, 2024
Psutil error when running sc.neighbors() in tutorial notebook scanpy		0	15	December 5, 2024
Error loading previously saved scVI model after updating packages / cloud environment scvi-tools		6	356	December 5, 2024
CUDA is available but Training scVI models is too slow scvi-tools scvi		4	38	December 4, 2024
Difference between differentialy expressed genes and violin plot scanpy		0	28	December 3, 2024
10X data import, "No such file or directory: features.tsv.gz" scanpy		0	35	November 29, 2024
Tensor nan error when training scANVI model Help scanvi , scvi		4	651	November 27, 2024
`crop0(sdata).pl.render_labels` running too slow spatialdata		1	20	November 27, 2024