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Issues: scverse/scanpy

Rename master -> main
#2869 by ivirshup was closed Feb 23, 2024
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501 Open 1,194 Closed
501 Open 1,194 Closed
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Issues list

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
Scatterplot with color for categorical value outputs attribute error about legend Bug 🐛 Needs info❔ More information needed
#3102 opened Jun 6, 2024 by albert239825
3 tasks done
3
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
4
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
Wrongly ordered DotPlot totals in scanpy 1.10.1 with Pandas 1.x Area - Plotting 🌺 Bug 🐛
#3062 opened May 16, 2024 by rgoya
2 of 3 tasks
1
@flying-sheep
3
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
Unexplainable sc.pp.highly_variable_genes(subset = True) behavior Bug 🐛
#3027 opened Apr 24, 2024 by jberkh
3 tasks done
1
@eroell
1
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 1.10.2
@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
Performance: Investigate pp.scale with sparse matrices Area – Performance 🐌 Enhancement ✨
#2986 opened Apr 8, 2024 by Intron7
1
Suggestion to support VisiumHD tissue_position_list files (using parquet files) Enhancement ✨
#2982 opened Apr 7, 2024 by Rafael-Silva-Oliveira
2
add support for Visium HD Spatial Gene Expression data Enhancement ✨
#2973 opened Apr 2, 2024 by 111-dep
1
9
Adding format checking for sparse matrix in the function "read_v3_10x_h5"
#2970 opened Mar 29, 2024 by CYQFWang
leiden alg with igraph flavor causes out of bounds freezing Bug 🐛
#2969 opened Mar 28, 2024 by RubenVanEsch
3 tasks done
1
@ilan-gold
19
Future warning in \preprocessing\_highly_variable_genes.py:226 Bug 🐛 Closing candidate Issue that can probably be closed
#2967 opened Mar 26, 2024 by dorzhey
2 of 3 tasks
3
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