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sc.tl.rank_genes_groups finds upregulated genes (lfc > 1.5) with pts 0
Bug 🐛
#2628
by noamharel161
was closed Jan 21, 2024
2 of 3 tasks
Create links between scanpy_tutorials and scanpy docs
Enhancement ✨
#922
by flying-sheep
was closed Jun 13, 2023
Reproducibility of regress_out() results
Bug 🐛
Needs info❔
More information needed
#1346
by marlena-D4C
was closed Oct 16, 2023
A bug about scanpy.pp.downsample_counts()
Bug 🐛
Needs info❔
More information needed
#1368
by AllenWu18
was closed Oct 16, 2023
3 tasks
Not able to select subset from clustered data which is added externally (k-means)
Enhancement ✨
#1452
by saiteja-danda
was closed Oct 23, 2023
KeyError: 'True: boolean label can not be used without a boolean index'
#1990
by brianpenghe
was closed Oct 12, 2023
Could not find keys in columns of adata.obs or in data.var_names
Closing candidate
Issue that can probably be closed
Needs info❔
More information needed
#2305
by pacificoceanmist
was closed Oct 12, 2023
2 of 3 tasks
Compatibility with latest python version
Needs info❔
More information needed
#2369
by YitengDang
was closed Dec 1, 2022
rank_genes_groups p value decimal places
Closing candidate
Issue that can probably be closed
Question
#1869
by mvis1231
was closed Oct 2, 2023
UMAP init_pos doesn't work with method rapids
Bug 🐛
#1837
by Intron7
was closed Aug 17, 2023
3 tasks done
PhenoGraph outputs Louvain method when using Leiden
Area – External
Dealing with external tools
Question
#2653
by prubbens
was closed Sep 5, 2023
2 of 3 tasks
PCA is hanging and taking way too long
Bug 🐛
Needs info❔
More information needed
#2531
by a-munoz-rojas
was closed Jul 7, 2023
2 of 3 tasks
pl.rank_genes_groups_violin() throws a KeyError when gene_symbols option is passed
Area - Plotting 🌺
Bug 🐛
#2540
by riederd
was closed Jul 7, 2023
2 of 3 tasks
read_visium() for newer SpaceRanger versions
Enhancement ✨
#2598
by deckerlin
was closed Aug 7, 2023
PMBC3k tutorial - issue loading saved object from .h5ad file
#2497
by tea-kostic
was closed Jun 7, 2023
2 of 3 tasks
Cluster content plot for integrated data
Enhancement ✨
Needs info❔
More information needed
#1573
by galicae
was closed Oct 29, 2023
1 of 5 tasks
sc.pl.spatial TypeError: can't multiply sequence by non-int of type 'float'
Area - IO
Reading and writing
Area – Spatial 🗺
#2499
by meaksu
was closed Jun 26, 2023
normalize_per_cell raises numpy.core._exceptions.UFuncTypeError
#2500
by scottgigante-immunai
was closed Jun 7, 2023
2 of 3 tasks
Unordered Categoricals can only compare equality or not
Bug 🐛
Needs info❔
More information needed
#1932
by Pawan291
was closed Oct 29, 2023
3 tasks
why there is not expression_cutoff in stacked violin plot
Enhancement ✨
Needs info❔
More information needed
#1871
by FADHLyemen
was closed Oct 29, 2023
5 tasks
dispersions_norm definition
Needs info❔
More information needed
Question
#1803
by moqri
was closed Oct 29, 2023
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