scverse scanpy issues - Githubissues

scverse / scanpy

Single-cell analysis in Python. Scales to >1M cells.

https://scanpy.readthedocs.io

BSD 3-Clause "New" or "Revised" License

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issues

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Use upstream sklearn PCA if possible

#3267 flying-sheep opened 3 days ago
1
sc.tl.score_genes -- ValueError: No valid genes were passed for scoring

#3266 xyang2uchicago opened 3 days ago
0
Backport PR #3264 on branch 1.10.x (Fix compat typing and old_positionals usage)

#3265 meeseeksmachine closed 3 days ago
1
Fix compat typing and old_positionals usage

#3264 flying-sheep closed 3 days ago
1
Implement sparse PCA using dask

#3263 flying-sheep opened 4 days ago
1
Add sanitize to score_genes

#3262 flying-sheep opened 4 days ago
1
AttributeError: Can only use .str accessor with string values!

#3261 DUAN-GAO opened 4 days ago
1
`regress_out` does not capture PerfectSeparation with statsmodels >= 0.14

#3260 jeskowagner opened 4 days ago
0
Backport PR #3258 on branch 1.10.x (Add `SIM` checks)

#3259 meeseeksmachine closed 5 days ago
0
Add `SIM` checks

#3258 flying-sheep closed 5 days ago
1
Backport PR #3256: [pre-commit.ci] pre-commit autoupdate

#3257 meeseeksmachine closed 6 days ago
1
[pre-commit.ci] pre-commit autoupdate

#3256 pre-commit-ci[bot] closed 6 days ago
1
Add scran nomalisation into scanpy

#3255 le-ander opened 1 week ago
2
Backport PR #3206 on branch 1.10.x (Fix *Plot.style() methods)

#3254 meeseeksmachine closed 1 week ago
1
Backport PR #3252 on branch 1.10.x (Deprecate defunct `order` parameter in `stacked_violin`)

#3253 meeseeksmachine closed 1 week ago
0
Deprecate defunct `order` parameter in `stacked_violin`

#3252 flying-sheep closed 1 week ago
1
Backport PR #3249 on branch 1.10.x (Clean up dendrogram typing)

#3251 meeseeksmachine closed 1 week ago
1
Auto-backport-of-pr-3248-on-1.10.x

#3250 flying-sheep closed 1 week ago
1
Clean up dendrogram typing

#3249 flying-sheep closed 1 week ago
1
Rely on Ruff for TYPE_CHECKING block mgmt

#3248 flying-sheep closed 1 week ago
1
Backport PR #3244 on branch 1.10.x (Finish `scale`→`density_norm` deprecation)

#3247 meeseeksmachine closed 1 week ago
1
Backport PR #3243 on branch 1.10.x (Fix stacked_violin’s `standard_scale` parameter)

#3246 meeseeksmachine closed 1 week ago
1
`io` submodule from `anndata`

#3245 ilan-gold opened 1 week ago
0
Finish `scale`→`density_norm` deprecation

#3244 flying-sheep closed 1 week ago
1
Fix stacked_violin’s `standard_scale` parameter

#3243 flying-sheep closed 1 week ago
1
Backport PR #3069: Upload scrublet scores on test failure

#3242 meeseeksmachine closed 1 week ago
1
Why making feature names unique instead of aggregation?

#3241 VladimirShitov opened 1 week ago
6
Backport PR #3239 on branch 1.10.x (Fix release note building and check)

#3240 meeseeksmachine closed 1 week ago
0
Fix release note building and check

#3239 flying-sheep closed 1 week ago
1
Backport PR #3235 on branch main ((chore): generate 1.10.3 release notes)

#3238 meeseeksmachine closed 1 week ago
1
Backport PR #3236 on branch 1.10.x (Fix towncrier git CLI call)

#3237 meeseeksmachine closed 1 week ago
0
Fix towncrier git CLI call

#3236 flying-sheep closed 1 week ago
0
(chore): generate 1.10.3 release notes

#3235 flying-sheep closed 1 week ago
1
Backport PR #3231 on branch 1.10.x (Switch to towncrier)

#3234 flying-sheep closed 1 week ago
1
Backport PR #3232 on branch 1.10.x ([pre-commit.ci] pre-commit autoupdate)

#3233 meeseeksmachine closed 1 week ago
1
[pre-commit.ci] pre-commit autoupdate

#3232 pre-commit-ci[bot] closed 1 week ago
1
Switch to towncrier

#3231 flying-sheep closed 1 week ago
1
Backport PR #3220 on branch 1.10.x (fa2 library changed to fa2_modified)

#3230 meeseeksmachine closed 2 weeks ago
1
Backport PR #3225: [pre-commit.ci] pre-commit autoupdate

#3229 meeseeksmachine closed 2 weeks ago
1
Leiden clustering does not seem to terminate

#3228 MichaelJFlynn closed 1 week ago
3
fix bug for partial_fit when the number of batch samples is less than n_comp

#3227 DingWB opened 2 weeks ago
2
Dask Sparse PCA

#3226 ilan-gold opened 2 weeks ago
0
[pre-commit.ci] pre-commit autoupdate

#3225 pre-commit-ci[bot] closed 2 weeks ago
1
pbmc68k_reduced raw counts

#3224 MartaBenegas opened 3 weeks ago
0
Backport PR #3213 on branch 1.10.x ([pre-commit.ci] pre-commit autoupdate)

#3223 meeseeksmachine closed 3 weeks ago
1
Backport PR #3216 on branch 1.10.x (Update notebooks)

#3222 meeseeksmachine closed 4 weeks ago
1
rank_genes_groups fails to account for multiple comparsions when multiple groups are provided.

#3221 a93sokol opened 4 weeks ago
0
fa2 library changed to fa2_modified

#3220 AminAlam closed 2 weeks ago
4
update source field on docs website

#3219 MishalAshraf closed 2 weeks ago
2
Backport PR #3217: (fix): Upper bound `dask`

#3218 meeseeksmachine closed 4 weeks ago
1