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Issues: scverse/scanpy

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

Type annotation considerations Question
#373 by flying-sheep was closed Nov 21, 2018
38
Export expression matrix from h5ad
#262 by cartal was closed Dec 21, 2018
30
Leiden now included in python-igraph
#1053 by vtraag was closed Feb 19, 2024 1.10.0
1
@ilan-gold
29
Adding Moran's I calculation to Scanpy Enhancement ✨
#1698 by Hrovatin was closed Nov 8, 2021
1
28
Clustering with leidenalg
#350 by ktpolanski was closed Sep 7, 2019
28
Where should sc.datasets put data?
#558 by ivirshup was closed Mar 31, 2019
26
Pre-commit (dev workflow) Enhancement ✨
#1563 by ivirshup was closed May 26, 2021 1.8.0
25
sc.read_h5ad randomly produces AnnDataReadError/OSError
#1351 by Hrovatin was closed Aug 1, 2020
25
var_names not being found by during plotting Area - Plotting 🌺 Bug 🐛 Needs info❔ More information needed
#1406 by bz520251 was closed Nov 15, 2021
24
TypeError: ufunc 'log1p' output (typecode 'd') could not be coerced to provided output parameter (typecode 'l') according to the casting rule ''same_kind''
#435 by ajitjohnson was closed Sep 2, 2020
1
24
Mitochondrial gene query not working with documented arguments
#242 by ivirshup was closed Nov 13, 2019
24
Cannot read loom file created in Seurat3 (column index exceeds matrix dimensions)
#598 by cakirb was closed Jun 5, 2019
23
highly_variable_genes(flavor='seurat') results differ from Seurat’s HVG results Enhancement ✨
#2780 by carversh was closed Feb 19, 2024
22
Runtime warning by rank_genes_groups
#653 by bioguy2018 was closed May 27, 2019
22
sc.pl.paga_path not working with TypeError Bug 🐛 Needs info❔ More information needed
#953 by mbuttner was closed Mar 1, 2021
1
21
highly_variable_genes - issue
#391 by ltosti was closed Dec 9, 2018
21
Calculate differential expression between user defined groups of clusters
#397 by aditisk was closed Dec 15, 2018
20
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
Contribution of scripts to scanpy main repo
#281 by pcm32 was closed Apr 16, 2019
1
19
scanpy conda installation error Bug 🐛
#990 by m21camby was closed Oct 28, 2021
18
Suggestion: Start a gitter.im chat room
#542 by outlace was closed Jul 8, 2019
18
Doublet filtering function Enhancement ✨ Help Wanted
#173 by yueqiw was closed Feb 12, 2024
1
18
Cannot import Scanpy Installation Windows
#2173 by charles-xu-ru was closed Jan 16, 2023
17
sc.tl.umap numba error when used with init_pos="paga"
#666 by jenzopr was closed May 29, 2019
17
setting gene_symbol to select symbol from adata.var fails in sc.pl.umap()
#455 by sebpott was closed Feb 1, 2019
17
ProTip! Follow long discussions with comments:>50.