Help

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

Topic		Replies	Views	Activity
About the Help category Help		0	302	March 4, 2022
Problem with airr data loading scirpy		9	66	September 28, 2023
Plotting only transcripts squidpy		3	15	September 27, 2023
Pl.ligrec error in latest version of squidpy squidpy		4	257	September 27, 2023
Re-integration after subseting cluster scvi-tools integration , scvi		2	48	September 26, 2023
Increase scVI integration speed scvi-tools integration		4	44	September 26, 2023
Deconvolute spatial (Visium) using a bulk RNA-seq dataset spatialdata		1	31	September 26, 2023
Sequential scArches scvi-tools integration , scvi , scarches		0	25	September 24, 2023
Gene shows up in dotplot, but it's not present in var_names scanpy plotting		1	37	September 16, 2023
scVI integration using two batch keys scvi-tools		4	67	September 15, 2023
Save layer back to spatialdata from napari spatialdata napari		5	33	September 15, 2023
How to save intermediate checkpoints? scvi-tools		1	102	September 14, 2023
How to install solo-sc or use hashsolo from scvi? scvi-tools		4	117	September 11, 2023
Get var_names used for training SCVI model scvi-tools scvi		0	36	September 11, 2023
Normalization on rpkm data scanpy		0	34	September 11, 2023
Is it possible to include leading edge genes in decoupler.run_gsea output? Help		3	162	September 8, 2023
How to properly save and load a TotalVI trained model that's based on mudata? muon totalvi		1	60	September 7, 2023
scVI reproducibility seed issue scvi-tools scvi		2	92	September 7, 2023
Error with import scvi Help scvi		2	60	September 7, 2023
The way to let pertpy use GPU Help		2	120	September 7, 2023
Error when saving adata with adata.write_h5ad(): "Above error raised while writing key 'names' of to /" scanpy		1	102	September 5, 2023
Error when draw UMAP: object has no attribute 'get_cmap' scanpy		4	273	September 5, 2023
Set dtype to np.float32 and memory conservation scanpy scvi		0	47	September 1, 2023
Comparing number of differentially expressed genes (DEGs) scanpy		0	76	August 31, 2023
Problems importing scvi [Windows] scvi-tools scvi		22	2577	August 29, 2023
TypeError when trying to set up scvi.model.TOTALVI() scvi-tools totalvi		2	71	August 29, 2023
Loading an scVI model from a pytorch lightning checkpoint scvi-tools scvi		3	135	August 29, 2023
Increase number of CPU cores for vae.train() in scvi? scvi-tools scvi , totalvi		3	87	August 28, 2023
Nonsense UMAP when including categorical covariates in a MULTIVI model Help scvi , multivi		1	80	August 28, 2023
Why scanpy computes HVGs based on the data after log1p? scanpy		0	53	August 28, 2023