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Issues: scverse/scanpy

Rename master -> main
#2869 by ivirshup was closed Feb 23, 2024
Closed 4
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504 Open 1,198 Closed
504 Open 1,198 Closed
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Issues list

cluster cells within groups when plotting with scanpy.pl.heatmap() Enhancement ✨ Triage 🩺 This issue needs to be triaged by a maintainer
#3129 opened Jun 28, 2024 by zsfrbkv
elem_mul in variance calculation should use float64 casting Bug 🐛 Triage 🩺 This issue needs to be triaged by a maintainer
#3127 opened Jun 26, 2024 by ilan-gold
3 tasks done
1.11.0
Fix all the various test failures
#3124 opened Jun 25, 2024 by flying-sheep
2 of 4 tasks
1.10.3
rank genes groups errors on less than 2 cells in a category Enhancement ✨ Triage 🩺 This issue needs to be triaged by a maintainer
#3118 opened Jun 22, 2024 by MishalAshraf
FindConservedMarkers implementaion in Scanpy Enhancement ✨ Triage 🩺 This issue needs to be triaged by a maintainer
#3117 opened Jun 22, 2024 by SNOL2
Unable to run Scrublet in v1.10 Bug 🐛
#3116 opened Jun 21, 2024 by jasonleongbio
2 of 3 tasks
3
Numpy 2 support (unpin) Enhancement ✨
#3114 opened Jun 20, 2024 by flying-sheep 1.10.3
1
@flying-sheep
Can't read in protein antibody capture data Bug 🐛 Triage 🩺 This issue needs to be triaged by a maintainer
#3113 opened Jun 18, 2024 by alexanderchang1
3 tasks done
Shuffled gene names for differential expression Bug 🐛 Triage 🩺 This issue needs to be triaged by a maintainer
#3106 opened Jun 13, 2024 by smithcathy
2 of 3 tasks
highly_variable_genes with batch_key results in a "division by zero" error, if there is a batch with a single sample Bug 🐛 Triage 🩺 This issue needs to be triaged by a maintainer
#3103 opened Jun 9, 2024 by YochayTzur
2 of 3 tasks
unexpected error in sc.pl.dpt_timeseries and dpt_groups_pseudotime Bug 🐛 Needs info❔ More information needed
#3086 opened Jun 2, 2024 by FessenSimon
2 of 3 tasks
2
Dotplot / Matrixplot Bug/Suggestion [Key Error] Because "var_group_labels" & "categories_order" using the same variable (memory), mostly happened when "swap_axes=True" Bug 🐛 Needs info❔ More information needed
#3081 opened May 31, 2024 by WhatMelonGua
3 tasks done
1
Adata.raw gets modified upon log normalization of adata Bug 🐛
#3073 opened May 22, 2024 by AlejandraRodelaRo
2 of 3 tasks
@flying-sheep
7
Error in running scrublet Bug 🐛 Needs info❔ More information needed
#3070 opened May 20, 2024 by dicklim
2 of 3 tasks
1
Broken Scrublet Test Bug 🐛
#3068 opened May 17, 2024 by ilan-gold
3 tasks done
1
@ilan-gold
sc.get.aggregate summary statistics Enhancement ✨
#3063 opened May 16, 2024 by grst
2
Access to Diffusion Map methods (and other embedding methods) as Scikit-Learn style API Area – API API design Enhancement ✨ Needs info❔ More information needed
#3054 opened May 14, 2024 by jolespin
2
Switch away from asv benchmark Enhancement ✨
#3052 opened May 13, 2024 by flying-sheep
@flying-sheep @ilan-gold
1
Loophole with using scaled adata for sc.tl.score_genes_cell_cycle
#3030 opened Apr 26, 2024 by kaushik-roy-physics
sc.pl.paga_path error in dimensions of array passed to ax.imshow Bug 🐛
#3025 opened Apr 23, 2024 by AlePur
2 of 3 tasks
Different clustering results when setting metrics = "cosine", using callable cosine function and direct cos distance input. Bug 🐛
#3021 opened Apr 22, 2024 by zby3
2 of 3 tasks
sc.pp.neighbors(..., knn=True, n_neighbors=k) does not threshold the adjacency Bug 🐛
#3014 opened Apr 18, 2024 by mkarikom
3 tasks done
Benchmarks: Add all from Dask tutorial benchmark
#3013 opened Apr 18, 2024 by flying-sheep 1.10.3
@flying-sheep
Pass n_iterations argument to scanpy.tl.louvain Enhancement ✨
#3007 opened Apr 15, 2024 by AlSzmigiel
@ivirshup
Failed violins Bug 🐛 Needs info❔ More information needed
#3005 opened Apr 12, 2024 by apodtele
2 of 3 tasks
@eroell
3
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