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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
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
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
Adata.raw gets modified upon log normalization of adata
Bug 🐛
#3073
opened May 22, 2024 by
AlejandraRodelaRo
2 of 3 tasks
Error in running scrublet
Bug 🐛
Needs info❔
More information needed
#3070
opened May 20, 2024 by
dicklim
2 of 3 tasks
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
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
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
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
Pass n_iterations argument to scanpy.tl.louvain
Enhancement ✨
#3007
opened Apr 15, 2024 by
AlSzmigiel
Failed violins
Bug 🐛
Needs info❔
More information needed
#3005
opened Apr 12, 2024 by
apodtele
2 of 3 tasks
Performance: Investigate
pp.scale
with sparse matrices
Area – Performance 🐌
Enhancement ✨
#2986
opened Apr 8, 2024 by
Intron7
Suggestion to support VisiumHD tissue_position_list files (using parquet files)
Enhancement ✨
#2982
opened Apr 7, 2024 by
Rafael-Silva-Oliveira
add support for Visium HD Spatial Gene Expression data
Enhancement ✨
#2973
opened Apr 2, 2024 by
111-dep
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
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
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