scverse/scanpy

#2390

· evanbiederstedt opened

on Dec 29, 2022

Column-wise `dask` `map_blocks`

Allow using arbitrary vectors in plotting (not only `obs` columns)

Area - Plotting 🌺

Area – API

Enhancement

#1500

· picciama opened

on Nov 18, 2020

Improve flexibility of `sc.pp.scrublet()`

Needs info❔

Bug

#3837

· zekepuli opened

on Oct 17, 2025

feature request for embedding_density()

Area - Plotting 🌺

Enhancement

#575

· sebpott opened

on Mar 30, 2019

Order of plotting datapoints with categorical colouring should be amended

Area - Plotting 🌺

Enhancement

#1263

· LuckyMD opened

on Jun 2, 2020

Spin off read/write into it's own package?

Question

#1387

· adamgayoso opened

on Aug 21, 2020

densmap

Enhancement

#1619

· ivirshup opened

on Feb 2, 2021

Inline example plots in docs

Area - Documentation 📒

Area - Plotting 🌺

good first issue

sc.pl.dotplot() `standard_scale='var'`: should scaling be changed?

Area - Plotting 🌺

Enhancement

#1757

· sjfleming opened

on Mar 22, 2021

STARsolo Matrix with Velocyto --> Anndata function

Enhancement

#1860

· JBreunig opened

on May 27, 2021

Public function for accessing category colors

Area - Plotting 🌺

Enhancement

#1881

· brianpenghe opened

on Jun 17, 2021

leiden and umap not reproducible on different CPUs

Area - Documentation 📒

Area – Reproducibility

Enhancement

#2014

· grst opened

on Oct 15, 2021

Compute UMAP from pre-existing distance matrix

Area - Topology 🍩

good first issue

Enhancement

#2157

· ivirshup opened

on Feb 25, 2022

Remove `sc.external`

Area – API

Area – External

Option to return sparse arrays from `sc.get.aggregate`

Area – API

Enhancement

#2898

· ivirshup opened

on Mar 6, 2024

cluster cells within groups when plotting with scanpy.pl.heatmap()

Area - Plotting 🌺

Enhancement

#3129

· zsfrbkv opened

on Jun 28, 2024

feature selection method using pearson residuals discrepancies

Question

Bug

#3452

· jflucier opened

on Jan 24, 2025

replace remaining utils with fast-array-utils

Development Process 🚀

Enhancement

#3784

· flying-sheep opened

on Sep 4, 2025

Highly Variable Genes Selection using CSC `dask`

Area - Out of core 💾

Area – Performance 🐌

Enhancement

#3862

· ilan-gold opened

on Oct 30, 2025

_sparse_nanmean is inefficient

Area – Performance 🐌

good first issue

Enhancement

#1894

· ivirshup opened

on Jun 22, 2021

`sc.external.pp.magic`: what is `n_jobs`'s default _really_?

#2387

· alexlenail opened

on Dec 27, 2022

Refactor `BasePlot` not to create a dataframe representation of the data

#3718

· ilan-gold opened

on Jul 18, 2025

`pp.regress_out` fails with to many CPU-Cores

Bug

#3910

· Intron7 opened

on Dec 11, 2025

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1.13.0

Call `numba.set_num_threads` when `n_jobs` is specified (e.g. in `scanpy.tl.rank_genes_group`)

feat: presets

Column-wise `dask` `map_blocks`

Allow using arbitrary vectors in plotting (not only `obs` columns)

Improve flexibility of `sc.pp.scrublet()`

feature request for embedding_density()

Order of plotting datapoints with categorical colouring should be amended

Spin off read/write into it's own package?

densmap

Inline example plots in docs

sc.pl.dotplot() `standard_scale='var'`: should scaling be changed?

STARsolo Matrix with Velocyto --> Anndata function

Public function for accessing category colors

leiden and umap not reproducible on different CPUs

Compute UMAP from pre-existing distance matrix

Remove `sc.external`

Option to return sparse arrays from `sc.get.aggregate`

cluster cells within groups when plotting with scanpy.pl.heatmap()

feature selection method using pearson residuals discrepancies

replace remaining utils with fast-array-utils

Highly Variable Genes Selection using CSC `dask`

_sparse_nanmean is inefficient

`sc.external.pp.magic`: what is `n_jobs`'s default _really_?

Refactor `BasePlot` not to create a dataframe representation of the data

`pp.regress_out` fails with to many CPU-Cores

1.13.0

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