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506 Open 1,278 Closed
506 Open 1,278 Closed
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Issues list

UMAP redesign Area - Topology 🍩 Neighbor graphs Area – API API design Meta A meta-request to be implemented in multiple steps
#3429 opened Jan 9, 2025 by flying-sheep
Support for scipy.csr_array/scipy.csc_array
#3423 opened Jan 1, 2025 by alam-shahul
2 of 3 tasks
4
Leiden clustering returns different results for Scanpy 1.10.4 and 1.9.3 Triage 🩺 This issue needs to be triaged by a maintainer
#3422 opened Dec 30, 2024 by alam-shahul
2 of 3 tasks
1
UMAP implementation in igraph
#3408 opened Dec 18, 2024 by iosonofabio
@ricor07
3
Allow both 'on data' legend together with legend on righ-hand side of plot Area - Plotting 🌺 Area – API API design
#3401 opened Dec 13, 2024 by mumichae
1
mask_obs parameter modifies obs column when calling scatterplot Area - Plotting 🌺
#3400 opened Dec 13, 2024 by mumichae
3 tasks done
1
cannot import name 'old_positionals' from 'scanpy._compat
#3390 opened Dec 2, 2024 by fbx233
2 of 3 tasks
1
"Interactive" Dotplot version: check for available var_names Area - Plotting 🌺
#3387 opened Nov 25, 2024 by FrancescaDr
1
Make _to_dense public?
#3386 opened Nov 25, 2024 by eroell
1
Difference between tl.rank_genes_groups and pl.rank_genes_groups_heatmap
#3378 opened Nov 20, 2024 by LioLenr
Nan values after running sc.tl.filter_rank_genes_groups and plotting
#3374 opened Nov 18, 2024 by shreyii
1
Switch to numpy.random.Generator Area – Reproducibility Exact replication
#3371 opened Nov 18, 2024 by flying-sheep
2 of 3 tasks
sc.pl.heatmap var_names function KeyError
#3363 opened Nov 13, 2024 by josenimo
3 tasks done
2
I started using scanny to read in data, but I always got the following error. I can't find any other detailed reasons.
#3355 opened Nov 12, 2024 by xzt199610
Dask docs Area - Documentation 📒 Area - Out of core 💾 Working with on disk data
#3346 opened Nov 8, 2024 by flying-sheep
@Intron7 @ilan-gold @mikelkou
1
Documentation typo for scanpy.pp.filter_cells
#3332 opened Oct 30, 2024 by fionaEyoung
ValueError: Output dtype not compatible with inputs. Needs info❔ More information needed
#3331 opened Oct 30, 2024 by ianfd
2 of 3 tasks
1
Feature Request: Option to Plot Highest Absolute Values on Top in sc.pl.umap Area - Plotting 🌺
#3326 opened Oct 25, 2024 by tobias-zehnder
scanpy.pl.stacked_violin - remove "marker label" whitespace if var_names is a list of genes Area - Plotting 🌺
#3320 opened Oct 24, 2024 by adkinsrs
3 tasks done
6
Multibatchnorm / between library batch normalization Area – Preprocessing 🧼
#3309 opened Oct 23, 2024 by Marwansha
2
negative values after score_genes with log1P or counts layer
#3297 opened Oct 20, 2024 by Li-ZhiD
Gearys C and Morans I As Public API
#3291 opened Oct 17, 2024 by ilan-gold
@Intron7
Plotting colors from obsm Area - Plotting 🌺
#3277 opened Oct 10, 2024 by canergen
1
ScanPy's BSD license and GPLed dependencies Question
#3272 opened Oct 1, 2024 by PertuyF
1
AttributeError: Can only use .str accessor with string values! Needs info❔ More information needed
#3261 opened Sep 26, 2024 by DUAN-GAO
2 of 3 tasks
3
ProTip! no:milestone will show everything without a milestone.