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Issues: scverse/scanpy

Rename master -> main
#2869 by ivirshup was closed Feb 23, 2024
Closed 4
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Issues list

New plot function to draw the relations between 2 categorical adata.obs variables? Enhancement ✨
#2797 opened Jan 3, 2024 by hyjforesight
1
Multiprocess for sc.tl.pca, sc.pp.neighbors, sc.tl.leiden, and sc.tl.umap
#2372 opened Nov 28, 2022 by hyjforesight
1 of 5 tasks
Is it possible to plot PCA for multiple samples?
#2356 opened Oct 19, 2022 by hyjforesight
plotting by sc.pl.dpt_timeseries(adata) has no colors
#2141 opened Feb 15, 2022 by hyjforesight
1
Store the BBKNN-proceeded embedding into individual obsm['X_umap']
#2123 by hyjforesight was closed Feb 22, 2022
4 tasks
1
UMAP is unreproducible between 3 Windows PCs Area – Reproducibility Exact replication Needs info❔ More information needed
#2114 opened Jan 19, 2022 by hyjforesight
14
Seurat uses log-transformed and scaled data for analysis, Scanpy uses raw, which method is better?
#2110 by hyjforesight was closed Jan 15, 2022
5
ImportError: DLL load failed while importing utilsextension
#2108 by hyjforesight was closed Jan 15, 2022
8
Unable to subset a new adata by highly variable genes Question
#2095 by hyjforesight was closed Jan 18, 2022
2
scikit-misc cannot be initiated when sc.pp.highly_variable_genes(adata, n_top_genes=5000, flavor='seurat_v3')
#2073 by hyjforesight was closed Jan 25, 2022
3 tasks done
19
leiden UMAP becomes grey and cannot be changed back Area - Plotting 🌺 good first issue easy first issue to get started in OSS community contribution! Question
#2058 by hyjforesight was closed Dec 8, 2021
1 task
5
logFC becomes negative and disappear for the top ranked genes when use_raw=False
#2057 opened Nov 23, 2021 by hyjforesight
1 task
How to show the downregulated marker genes by sc.pl.rank_genes_groups?
#2052 by hyjforesight was closed Nov 23, 2021
4 tasks
1
Adding use_raw=False create errors Area - Plotting 🌺 Area - Raw 🍣 Area – Differential Expression Differential expression Needs info❔ More information needed
#2046 by hyjforesight was closed Nov 8, 2021
3
UMAP goes wrong on scanpy v1.7.2 Upstream
#2045 by hyjforesight was closed Nov 8, 2021
5
Why we cannot tranfer adata along with functions?
#2030 by hyjforesight was closed Dec 14, 2021
1
Which data should be used for finding marker genes?
#2029 by hyjforesight was closed Dec 30, 2021
4
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