Skip to content

Issues: scverse/scanpy

Rename master -> main
#2869 by ivirshup was closed Feb 23, 2024
Closed 4
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

501 Open 1,179 Closed
501 Open 1,179 Closed
Author
Filter by author
Label
Filter by label
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Milestones
Filter by milestone
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Broken Scrublet Test Bug 🐛 Triage 🩺 This issue needs to be triaged by a maintainer
#3068 opened May 17, 2024 by ilan-gold
3 tasks done
1
@ilan-gold
sc.get.aggregate summary statistics Enhancement ✨ Triage 🩺 This issue needs to be triaged by a maintainer
#3063 opened May 16, 2024 by grst
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
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
More complete dataset documentation Area - Documentation 📒 Enhancement ✨
#3051 opened May 13, 2024 by flying-sheep
1
2
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
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
1
@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
ProTip! no:milestone will show everything without a milestone.