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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Backport PR #3329 on branch 1.10.x ([pre-commit.ci] pre-commit autoupdate)

#3338 meeseeksmachine closed 3 weeks ago
1
Actually working min-deps job

#3337 flying-sheep closed 1 week ago
1
Fix PCA tests

#3336 flying-sheep closed 3 weeks ago
2
move all `njit` calls into a decorator

#3335 flying-sheep closed 2 weeks ago
3
Backport PR #3328 on branch 1.10.x (Align `get.obs_df`’s docs with its code)

#3334 meeseeksmachine closed 3 weeks ago
1
(fix): sort pca test args

#3333 ilan-gold closed 3 weeks ago
3
Documentation typo for scanpy.pp.filter_cells

#3332 fionaEyoung opened 3 weeks ago
0
ValueError: Output dtype not compatible with inputs.

#3331 ianfd opened 3 weeks ago
1
~ 35.63% faster filtering

#3330 kaushalprasadhial opened 4 weeks ago
1
[pre-commit.ci] pre-commit autoupdate

#3329 pre-commit-ci[bot] closed 3 weeks ago
1
Align `get.obs_df`’s docs with its code

#3328 flying-sheep closed 3 weeks ago
4
Backport PR #3285 on branch 1.10.x (Update `test_rank_genes_groups.py` reference)

#3327 meeseeksmachine closed 4 weeks ago
0
Feature Request: Option to Plot Highest Absolute Values on Top in sc.pl.umap

#3326 tobias-zehnder opened 1 month ago
0
Remove calls to `.format`

#3325 flying-sheep opened 1 month ago
1
Support `layer` in `sc.pl.highest_expr_genes`

#3324 flying-sheep closed 3 weeks ago
1
Backport PR #3321 on branch 1.10.x (Enforce `np.bool_` usage via Ruff)

#3323 meeseeksmachine closed 1 month ago
0
Backport PR #3316 on branch 1.10.x (Refactor regress_out)

#3322 meeseeksmachine closed 1 month ago
0
Enforce `np.bool_` usage via Ruff

#3321 flying-sheep closed 1 month ago
1
scanpy.pl.stacked_violin - remove "marker label" whitespace if var_names is a list of genes

#3320 adkinsrs opened 1 month ago
6
Benchmark dask

#3319 mikelkou opened 1 month ago
2
sc.pl.highest_expr_genes() with layer errors

#3318 mezwick closed 3 weeks ago
3
Fix zappy compatibility for clip_array

#3317 flying-sheep closed 2 weeks ago
1
Refactor regress_out

#3316 flying-sheep closed 1 month ago
2
Move PSE outside try except

#3315 Zethson closed 1 month ago
4
Backport PR #3275 on branch 1.10.x (Catch PerfectSeparationWarning during regress_out)

#3314 meeseeksmachine closed 1 month ago
1
fix bug for partial_fit when the number of batch samples is less than n_comp

#3313 DingWB opened 1 month ago
0
Backport PR #3311 on branch 1.10.x (Fix some `Returns` docstrs re: `inplace` semantics)

#3312 meeseeksmachine closed 1 month ago
1
Fix some `Returns` docstrs re: `inplace` semantics

#3311 ryan-williams closed 1 month ago
1
Improve input descriptions for scanpy.get.obs_df

#3310 emdann closed 3 weeks ago
1
Multibatchnorm / between library batch normalization

#3309 Marwansha opened 1 month ago
0
Backport PR #3302: Fix sc.pl.highest_expr_genes with a categorical column

#3308 meeseeksmachine closed 1 month ago
1
(feat): `calculate_qc_metrics` with `dask`

#3307 ilan-gold closed 2 weeks ago
5
(fix): clarify sparse pca usage

#3306 ilan-gold closed 1 month ago
1
Backport PR #3274 on branch 1.10.x ([pre-commit.ci] pre-commit autoupdate)

#3305 meeseeksmachine closed 1 month ago
1
Backport PR #3298 on branch 1.10.x ((fix): correct anndata release for `io` usage)

#3304 meeseeksmachine closed 1 month ago
1
Backport PR #3283 on branch 1.10.x (Remove 3.9 support)

#3303 flying-sheep closed 1 month ago
1
Fix sc.pl.highest_expr_genes with a categorical column

#3302 flying-sheep closed 1 month ago
1
Backport PR #3299: Allow specifying a collection of colors to scatterplots

#3301 flying-sheep closed 1 month ago
1
Backport PR #3286 on branch 1.10.x (Fix HVG with 1-obs batches)

#3300 meeseeksmachine closed 1 month ago
0
Allow specifying a collection of colors to scatterplots

#3299 flying-sheep closed 1 month ago
3
(fix): correct anndata release for `io` usage

#3298 ilan-gold closed 1 month ago
1
negative values after score_genes with log1P or counts layer

#3297 Li-ZhiD opened 1 month ago
0
Add explicit support to PCA for `'covariance_eigh'` svd_solver

#3296 flying-sheep closed 1 month ago
1
lets umap run in parallel

#3295 Intron7 opened 1 month ago
2
Test all PCA param combinations

#3294 flying-sheep closed 1 month ago
1
Backport PR #3292 on branch 1.10.x (Fix benchmark job: Use upstream asv)

#3293 meeseeksmachine closed 1 month ago
0
Fix benchmark job: Use upstream asv

#3292 flying-sheep closed 1 month ago
1
Gearys C and Morans I As Public API

#3291 ilan-gold opened 1 month ago
0
Backport PR #3289 on branch 1.10.x ((fix): conditional imports to avoid `anndata.io` warning)

#3290 meeseeksmachine closed 1 month ago
1
(fix): conditional imports to avoid `anndata.io` warning

#3289 ilan-gold closed 1 month ago
1

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