Help

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

Topic	Replies	Views	Activity
About the Help category Help	0	145	March 4, 2022
Scvi-toools based model does not log metrics on every step scvi-tools	1	4	February 3, 2023
Correct use of .copy() when working with layers scanpy	0	9	February 2, 2023
Umap results not comparable Help	2	5	February 2, 2023
Avoiding AnnData.file._adata self-reference? anndata	0	8	February 2, 2023
Guidelines to use scanpy layers scanpy	3	80	February 2, 2023
Does processing the data always overwrite the raw counts? scanpy	0	7	February 2, 2023
Unstable result scvi-tools scvi	0	8	February 1, 2023
Changing parameters in scanpy's scanpy._settings.ScanpyConfig scanpy	0	7	February 1, 2023
Show cluster numbers on scanpy UMAP plot like in Featureplot in Seurat scanpy scrna-seq , plotting	3	141	January 30, 2023
Transform_batch parameter of scVI's get_normalized_expression scvi-tools scvi	2	51	January 28, 2023
Differential expression filtering in scVI scvi-tools	0	22	January 26, 2023
Log metrics from a Pyro model scvi-tools	2	15	January 26, 2023
Scanpy.external.tl.phenograph scanpy	3	33	January 26, 2023
Adata.obs entries for specific layers anndata	2	63	January 26, 2023
Zstack with images having different sizes squidpy	0	15	January 26, 2023
Anndata.write fails with "object header message is too large" anndata	3	155	January 26, 2023
totalVI, peakVI, multiVI with scRNA-seq and scATAC-seq data scvi-tools multivi , totalvi , modeling	2	186	January 24, 2023
Ambient RNA Filtering with scAR prior to scVI scvi-tools scvi	1	51	January 23, 2023
Re-integrate after removing low-quality cells? scvi-tools scvi	2	50	January 23, 2023
Best way to rank genes for GSEA analysis scvi-tools diff-exp , scvi	1	40	January 23, 2023
Writing/reading scANVI model error? scvi-tools	3	35	January 23, 2023
How to handle data lognormalization when using highly_variable_genes() with flavor seurat_v3? scanpy	1	25	January 23, 2023
How to create a layer over a subset of .obs or .vars? anndata developer	1	45	January 20, 2023
Multiple training sets with scVI? scvi-tools integration , scvi	1	41	January 20, 2023
Differential Expression using Scanpy scanpy	1	97	January 18, 2023
Silence verbose logging during scVI training scvi-tools	0	27	January 18, 2023
Error running ModelTuner.fit scvi-tools	4	67	January 17, 2023
Choosing a Dispersion Option in scvi Model Training scvi-tools	0	19	January 17, 2023
"Vanilla" vs "Change" Mode in Differential Expression scvi-tools diff-exp	2	45	January 17, 2023