Help

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

Topic	Replies	Views	Activity
About the Help category Help	0	169	March 4, 2022
"ValueError: cannot specify integer `bins` when input data contains infinity" in multi sample data scanpy integration , multivi	4	61	March 30, 2023
How to check average gene expression for each of 2 conditions within a cluster in scanpy? Help	0	11	March 30, 2023
Plotting repertoire overlap as a heatmap with scirpy scirpy plotting	2	16	March 29, 2023
Hyperparameter optimization of SCVI model using the autotune package scvi-tools	3	48	March 28, 2023
Squidpy comparative statistics squidpy	2	61	March 28, 2023
Centrality Score: Understanding average clustering squidpy	1	82	March 28, 2023
scANVI relables known cells with known types incorrectly scvi-tools scanvi	12	698	March 28, 2023
Problems subsetting scanpy	0	19	March 27, 2023
About model.differential analysis scvi-tools diff-exp , scvi	0	19	March 26, 2023
Tuning/setting scvi.model.SCVI parameters scvi-tools scvi	9	361	March 25, 2023
DE analysis between two batch-specific clusters scvi-tools diff-exp , scvi	9	278	March 24, 2023
Batch correction in reconstructed gene space scvi-tools	4	45	March 24, 2023
Choosing a Dispersion Option in scvi Model Training scvi-tools	1	66	March 23, 2023
Subclustering of one single cluster in my UMAP Plot scanpy clustering	0	24	March 23, 2023
Is anndata limited to 2d data? anndata	1	35	March 22, 2023
Question about Github Issue scanpy developer	2	65	March 22, 2023
UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored scanpy scvi , developer	4	312	March 22, 2023
Make another probabilistic model in scvi-tools scvi-tools developer	2	91	March 22, 2023
How to load the AKOYA(CODEX) processor pipeline outputs a csv files for Squidpy? squidpy	2	105	March 22, 2023
How to read in the Spatial object directly from gene count matrix (.mtx) file and related images (without HDF5 file)? scanpy	0	18	March 22, 2023
How to assign the specific colors to cell types on umaps across different dataset? scanpy	2	29	March 20, 2023
GPU available but not using scvi-tools	7	231	March 17, 2023
Building machine learning model for lectin array scvi-tools	0	30	March 17, 2023
How to make a UMAP for single cell data and color cells by average expression of a list of genes in scanpy? scanpy	1	123	March 16, 2023
Subsetting anndata is causing error problems scanpy	1	51	March 16, 2023
Scanpy HVG batch_key scanpy	1	69	March 16, 2023
Read_10x_mtx error UnicodeDecodeError: scanpy	1	65	March 16, 2023
Subsetting populations scanpy	1	52	March 16, 2023
Identifying pseudotime-associated genes with GAM Help	1	84	March 16, 2023