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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A memory efficient implementation of the .mtx reading function

#3389 gjeuken opened 1 day ago
1
[pre-commit.ci] pre-commit autoupdate

#3388 pre-commit-ci[bot] opened 4 days ago
1
"Interactive" Dotplot version: check for available var_names

#3387 FrancescaDr opened 4 days ago
0
Make _to_dense public?

#3386 eroell opened 4 days ago
0
sc.tl.rank_genes_groups on integrated counts

#3385 Prakrithi-P closed 1 day ago
1
Switch to session-info2

#3384 flying-sheep opened 1 week ago
1
Backport PR #3372: Deprecate RandomState (using names only)

#3383 flying-sheep closed 1 week ago
1
Backport PR #3380: Use deprecation decorator

#3382 flying-sheep closed 1 week ago
1
current scanpy v1.10.3 cannot import igraph dependencies for sc.tl.leiden clustering algo

#3381 billiegould closed 1 week ago
2
Use deprecation decorator

#3380 flying-sheep closed 1 week ago
1
remove out of core median

#3379 Intron7 opened 1 week ago
2
Difference between tl.rank_genes_groups and pl.rank_genes_groups_heatmap

#3378 LioLenr opened 1 week ago
0
Rank genes groups wilcoxon test fails for more than 10 million cells

#3377 abs51295 opened 1 week ago
0
Backport PR #3362 on branch 1.10.x (Updated Harmony Integrate Docs to better match interface to Harmonypy package)

#3376 meeseeksmachine closed 1 week ago
1
Backport PR #3373: [pre-commit.ci] pre-commit autoupdate

#3375 meeseeksmachine closed 1 week ago
1
Nan values after running sc.tl.filter_rank_genes_groups and plotting

#3374 shreyii opened 1 week ago
1
[pre-commit.ci] pre-commit autoupdate

#3373 pre-commit-ci[bot] closed 1 week ago
1
Deprecate RandomState (using names only)

#3372 flying-sheep closed 1 week ago
1
Switch to `numpy.random.Generator`

#3371 flying-sheep opened 1 week ago
0
Error in Scanpy Doublet Analysis with Scrublet on .h5ad Data Using backed="r+"

#3370 simang5c closed 3 days ago
1
Backport PR #3364 on branch 1.10.x (Fix CI)

#3369 meeseeksmachine closed 2 weeks ago
0
Add `mask` to `sc.pp.subsample`

#3368 flying-sheep opened 2 weeks ago
0
Constrain all extras for min-deps job

#3367 flying-sheep opened 2 weeks ago
1
Backport PR #3337 on branch 1.10.x (Actually working min-deps job)

#3366 meeseeksmachine closed 2 weeks ago
1
faster reading of h5ad file (~18X faster)

#3365 kaushalprasadhial opened 2 weeks ago
1
Fix CI

#3364 flying-sheep closed 2 weeks ago
1
sc.pl.heatmap var_names function KeyError

#3363 josenimo opened 2 weeks ago
1
Updated Harmony Integrate Docs to better match interface to Harmonypy package

#3362 DaminK closed 1 week ago
2
Updated Harmony Integrate Docs to better match interface to Harmonypy package

#3361 DaminK closed 2 weeks ago
1
Fix “preprocessing” docs page

#3360 flying-sheep opened 2 weeks ago
0
Backport PR #3357 on branch main ((chore): generate 1.10.4 release notes)

#3359 meeseeksmachine closed 2 weeks ago
0
Backport PR #3354: [pre-commit.ci] pre-commit autoupdate

#3358 meeseeksmachine closed 2 weeks ago
1
(chore): generate 1.10.4 release notes

#3357 flying-sheep closed 2 weeks ago
2
(chore): generate 1.10.4 release notes

#3356 flying-sheep closed 2 weeks ago
1
I started using scanny to read in data, but I always got the following error. I can't find any other detailed reasons.

#3355 xzt199610 opened 2 weeks ago
0
[pre-commit.ci] pre-commit autoupdate

#3354 pre-commit-ci[bot] closed 2 weeks ago
1
Create cat regressor

#3353 Intron7 opened 2 weeks ago
2
Backport PR #3317 on branch 1.10.x (Fix zappy compatibility for clip_array)

#3352 flying-sheep closed 2 weeks ago
1
Simplify scale

#3351 flying-sheep opened 2 weeks ago
2
Backport PR #3284 on branch 1.10.x (Speedup (~20x) of scanpy.pp.regress_out function using Linear Least Square method.)

#3350 meeseeksmachine closed 2 weeks ago
1
Update notebooks

#3349 flying-sheep closed 2 weeks ago
1
Implementation of fireducks pandas

#3348 KarlKaise opened 2 weeks ago
0
Change default matplotlib.rcParams["axes.grid"] from True to False

#3347 senseibence opened 2 weeks ago
2
Dask docs

#3346 flying-sheep opened 3 weeks ago
0
scanpy installation on colab without any GPU's

#3345 CRISTIANJULIOCESAR opened 3 weeks ago
3
Backport PR #3343 on branch 1.10.x (Fix docs)

#3344 meeseeksmachine closed 3 weeks ago
0
Fix docs

#3343 flying-sheep closed 3 weeks ago
1
Cannot read Visium HD data using spatialdata-io (Recurrent error). Data is non-zarr format.

#3342 ankshe91 opened 3 weeks ago
11
Issues with reading in non zarr format Visium HD data in python

#3341 ankshe opened 3 weeks ago
0
(feat): seurat v3 with dask

#3340 ilan-gold opened 3 weeks ago
1