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Issues: scverse/scanpy

Rename master -> main
#2869 by ivirshup was closed Feb 23, 2024
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496 Open 1,177 Closed
496 Open 1,177 Closed
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Issues list

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
AttributeError: module 'scanpy.preprocessing' has no attribute 'scrublet' Bug 🐛
#3026 opened Apr 23, 2024 by bingy007
3 tasks done
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
Benchmarks: Add all from basic tutorial benchmark
#3012 opened Apr 18, 2024 by flying-sheep 1.10.2
1
@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
AxisError when calculating QC metrics on backed data Bug 🐛
#3004 opened Apr 12, 2024 by dn-ra
2 of 3 tasks
@ilan-gold
1
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
pl.rank_genes_groups_violin should be able to pass **kwds to pl.violin Enhancement ✨
#2954 opened Mar 25, 2024 by jpintar
Dask support for normalize_pearson_residuals, highly_variable_genes(flavor='pearson_residuals') Area - Out of core 💾 Working with on disk data Area – Performance 🐌 Enhancement ✨
#2940 opened Mar 21, 2024 by eroell
1
@eroell
NMF Enhancement ✨
#2939 opened Mar 21, 2024 by ivirshup
calculate_qc_metrics for dask Enhancement ✨
#2937 opened Mar 21, 2024 by ilan-gold 1.11.0
Add layer argument to score_genes()/score_genes_cell_cycle() Area – API API design Enhancement ✨
#2910 opened Mar 14, 2024 by lazappi 1.11.0
1
1
Document input in score_genes()/score_genes_cell_cycle() Enhancement ✨
#2909 opened Mar 14, 2024 by lazappi
1
Get modularity score after community detection in leiden/louvain Enhancement ✨
#2908 opened Mar 13, 2024 by AlSzmigiel 1.11.0
3
sc.tl.leiden, restrict_to function not properly working Area - Topology 🍩 Neighbor graphs Bug 🐛 Needs info❔ More information needed
#2906 opened Mar 12, 2024 by simonekats
3 tasks done
1
ProTip! What’s not been updated in a month: updated:<2024-04-07.