Help

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

Topic		Replies	Views	Activity
About the Help category Help		0	472	March 4, 2022
Insufficient batch correction for certain cell-types scvi-tools integration , scvi		5	42	April 26, 2024
Computing neighbors from X_scANVI representation scvi-tools scanvi , scvi		5	136	April 26, 2024
Early stopping debug scvi-tools		1	22	April 26, 2024
Benchmarking CellHint with scib-metrics Benchmarker tool how to use embedding_obsm_keys Help scrna-seq , scanvi , scvi , integration		1	36	April 25, 2024
Confused about hyperparam tuning in scVI scvi-tools scvi		1	54	April 25, 2024
Scvi model training after sub-clustering scvi-tools integration , scvi		1	54	April 25, 2024
Computing sc.pp.neighbors without method? scanpy		2	268	April 25, 2024
How can I logarithmize the data for wilcoxon test? scanpy		1	25	April 25, 2024
scvi.model.SCVI input values scvi-tools integration , scvi		1	35	April 23, 2024
Does processing the data always overwrite the raw counts? scanpy		3	1433	April 22, 2024
Question about diffusion map "gaussian" implementation scanpy		2	194	April 19, 2024
SOLO/scVI .train() error related to batch_size? scvi-tools scvi		3	642	April 3, 2024
How to add splice/unspliced layers to h5ad object Help		0	22	April 20, 2024
How to interpret Diffusion Maps? scanpy		0	44	April 18, 2024
Managing anndata with multiple features from each gene anndata		4	44	April 17, 2024
How can I export list of genes and counts for each cluster from adata.raw? scanpy		1	89	April 12, 2024
Cannot load filtered_contig_annotations.csv scirpy		1	36	April 12, 2024
Change the font family for scanpy.pl in linux scanpy		1	51	April 11, 2024
Remove coordinate system from Spatialdata spatialdata		1	42	April 9, 2024
Cell charter niche calling Help		3	53	April 9, 2024
Anndata.concat([a,b], join="inner") does not behave as a.concat(b) anndata integration , anndata		0	34	April 8, 2024
Environment recipes for scVI autotune and scIB-metrics Benchmarker scvi-tools		0	54	April 7, 2024
Is anndata limited to 2d data? anndata		3	268	April 5, 2024
Napari_spatialdata colouring cell_labels and plotting specific transcripts spatialdata		1	64	April 5, 2024
scRNA-seq batch correction for DestVI scvi-tools destvi , scvi-tools		2	93	April 3, 2024
TCR and BCR genes and HVGs selection scanpy scvi		5	92	April 3, 2024
Issues setting up anndata for SCVI anndata scvi , integration		2	105	April 2, 2024
Differential expression genes: test to use? scanpy diff-exp		0	73	April 2, 2024
Leiden clustering gives me different results when I run it scanpy		1	93	April 1, 2024