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rank_genes_groups logfoldchange different than seurat

Status: Open.

#864 In scverse/scanpy;

· nagaBoulevard opened on Oct 7, 2019

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

Area – Differential ExpressionDifferential expressionDifferential expression

Area – Performance 🐌

Status: Open.

Enhancement

#2390 In scverse/scanpy;

· evanbiederstedt opened on Dec 29, 2022

Column-wise dask map_blocks

MetaA meta-request to be implemented in multiple stepsA meta-request to be implemented in multiple steps

Status: Open.

Enhancement

#3723 In scverse/scanpy;

· ilan-gold opened on Jul 21, 2025

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

Area - Plotting 🌺

Area – APIAPI designAPI design

Status: Open.

Enhancement

#1500 In scverse/scanpy;

· picciama opened on Nov 18, 2020

Improve flexibility of sc.pp.scrublet()

Needs info❔More information neededMore information needed

Status: Open.

Bug

#3837 In scverse/scanpy;

· ghost opened on Oct 17, 2025

feature request for embedding_density()

Area - Plotting 🌺

Status: Open.

Enhancement

#575 In scverse/scanpy;

· sebpott opened on Mar 30, 2019

Order of plotting datapoints with categorical colouring should be amended

Area - Plotting 🌺

Status: Open.

Enhancement

#1263 In scverse/scanpy;

· LuckyMD opened on Jun 2, 2020

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

Question

Status: Open.

#1387 In scverse/scanpy;

· adamgayoso opened on Aug 21, 2020

densmap

Status: Open.

Enhancement

#1619 In scverse/scanpy;

· ivirshup opened on Feb 2, 2021

Inline example plots in docs

Area - Documentation 📒

Area - Plotting 🌺

good first issueeasy first issue to get started in OSS community contribution!easy first issue to get started in OSS community contribution!

MetaA meta-request to be implemented in multiple stepsA meta-request to be implemented in multiple steps

Status: Open.

Enhancement

#1664 In scverse/scanpy;

· ivirshup opened on Feb 19, 2021

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

Area - Plotting 🌺

Status: Open.

Enhancement

#1757 In scverse/scanpy;

· sjfleming opened on Mar 22, 2021

STARsolo Matrix with Velocyto --> Anndata function

Status: Open.

Enhancement

#1860 In scverse/scanpy;

· JBreunig opened on May 27, 2021

Public function for accessing category colors

Area - Plotting 🌺

Status: Open.

Enhancement

#1881 In scverse/scanpy;

· brianpenghe opened on Jun 17, 2021

leiden and umap not reproducible on different CPUs

Area - Documentation 📒

Area – ReproducibilityExact replicationExact replication

Status: Open.

Enhancement

#2014 In scverse/scanpy;

· grst opened on Oct 15, 2021

Compute UMAP from pre-existing distance matrix

Area - Topology 🍩Neighbor graphsNeighbor graphs

good first issueeasy first issue to get started in OSS community contribution!easy first issue to get started in OSS community contribution!

Status: Open.

Enhancement

#2157 In scverse/scanpy;

· ivirshup opened on Feb 25, 2022

Remove sc.external

Area – APIAPI designAPI design

Area – ExternalDealing with external toolsDealing with external tools

MetaA meta-request to be implemented in multiple stepsA meta-request to be implemented in multiple steps

Status: Open.

#2717 In scverse/scanpy;

· flying-sheep opened on Oct 26, 2023

Option to return sparse arrays from sc.get.aggregate

Area – APIAPI designAPI design

Status: Open.

Enhancement

#2898 In scverse/scanpy;

· ivirshup opened on Mar 6, 2024

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

Area - Plotting 🌺

Status: Open.

Enhancement

#3129 In scverse/scanpy;

· zsfrbkv opened on Jun 28, 2024

feature selection method using pearson residuals discrepancies

Question

Status: Open.

Bug

#3452 In scverse/scanpy;

· jflucier opened on Jan 24, 2025

replace remaining utils with fast-array-utils

Development Process 🚀

Status: Open.

Enhancement

#3784 In scverse/scanpy;

· flying-sheep opened on Sep 4, 2025

Highly Variable Genes Selection using CSC dask

Area - Out of core 💾Working with on disk dataWorking with on disk data

Area – Performance 🐌

Status: Open.

Enhancement

#3862 In scverse/scanpy;

· ilan-gold opened on Oct 30, 2025

_sparse_nanmean is inefficient

Area – Performance 🐌

good first issueeasy first issue to get started in OSS community contribution!easy first issue to get started in OSS community contribution!

Status: Open.

Enhancement

#1894 In scverse/scanpy;

· ivirshup opened on Jun 22, 2021

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

Status: Open.

#2387 In scverse/scanpy;

· alexlenail opened on Dec 27, 2022

Refactor BasePlot not to create a dataframe representation of the data

Area - Plotting 🌺

Area – Performance 🐌

good first issueeasy first issue to get started in OSS community contribution!easy first issue to get started in OSS community contribution!

Status: Open.

Enhancement

#3718 In scverse/scanpy;

· ilan-gold opened on Jul 18, 2025

pp.regress_out fails with to many CPU-Cores

Status: Open.

Bug

#3910 In scverse/scanpy;

· Intron7 opened on Dec 11, 2025