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Running sc.pp.highly_variable_genes(adata, n_top_genes=5000, flavor='seurat_v3') produces scikit-misc error; package not installable with either pip or conda
Question
#3144
by DNApolymerase3
was closed Jul 8, 2024
3 tasks done
sc.pp.neighbors error: api_export.__init__() got an unexpected keyword argument 'metaclass'
Bug 🐛
Triage 🩺
This issue needs to be triaged by a maintainer
#3143
by Rafael-Silva-Oliveira
was closed Jul 4, 2024
2 of 3 tasks
AttributeError (sc.pl.stacked_violin)
Bug 🐛
Triage 🩺
This issue needs to be triaged by a maintainer
#3140
by JelenaKrneta
was closed Jul 3, 2024
2 of 3 tasks
Scatterplot with color for categorical value outputs attribute error about legend
Bug 🐛
#3102
by albert239825
was closed Jun 13, 2024
3 tasks done
scanpy.pl.spatial plotting square pixels
Question
Triage 🩺
This issue needs to be triaged by a maintainer
#3096
by HaikuoLi
was closed Jun 7, 2024
scanpy legacy and not legacy about scale
Question
#3095
by asmlgkj
was closed Jun 7, 2024
2 of 3 tasks
OSError between tissue_positions_list.csv and tissue_positions.csv
Bug 🐛
#3085
by alexanderchang1
was closed Jun 7, 2024
2 of 3 tasks
Pre-release jobs fail because scipy removed
.A from csr/csc matrices
Bug 🐛
#3083
by flying-sheep
was closed Jun 3, 2024
2 of 3 tasks
I have always had a question: do I need to scale my adata before running sc.tl.score_genes?
Question
#3080
by christophechu
was closed Jun 7, 2024
3 tasks done
Only show the genes that have significant statistics
Enhancement ✨
#3077
by ngvananh2508
was closed Jun 7, 2024
error in readwrite.py
Bug 🐛
Triage 🩺
This issue needs to be triaged by a maintainer
#3071
by JonatanSahar
was closed May 20, 2024
2 of 3 tasks
More complete dataset documentation
Area - Documentation 📒
Enhancement ✨
#3051
by flying-sheep
was closed Jun 4, 2024
will rank_genes_groups_dotplot support results from filter_rank_genes_groups?
Area - Documentation 📒
#3049
by Li-ZhiD
was closed May 13, 2024
When importing Scanpy 1.9.1, if you're using matplotlib version below 3.7, you might encounter a metaclass error.
Bug 🐛
#3029
by 12hsk
was closed Apr 25, 2024
3 tasks done
sc.tl.leiden with Exact replication
Bug 🐛
Needs info❔
More information needed
flavor='igraph' raises an (ignored by igraph) “ValueError: high is out of bounds for int32”
Area – Reproducibility
#3028
by hl324
was closed May 2, 2024
2 of 3 tasks
AttributeError: module 'scanpy.preprocessing' has no attribute 'scrublet'
Bug 🐛
#3026
by bingy007
was closed May 19, 2024
3 tasks done
Add a needs triage tag
Development Process 🚀
Enhancement ✨
#3010
by ivirshup
was closed Apr 30, 2024
sc.tl.leiden TypeError: unexpected keyword 'flavor'
Bug 🐛
Closing candidate
Issue that can probably be closed
#2981
by hl324
was closed Apr 11, 2024
2 of 3 tasks
AssertionError: Don’t call _normalize_index with non-categorical/string names
Bug 🐛
#2979
by alexlenail
was closed Apr 4, 2024
2 of 3 tasks
sc.tl.ingest: pkg_version does not work with anndata==0.10.6
Bug 🐛
Installation
Needs info❔
#2978
by maarten-devries
was closed Apr 8, 2024
3 tasks done
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Updated in the last three days: updated:>2024-07-07.