Issues

• downsample_counts(total_counts=...) silently does nothing for Fortran-ordered dense X

  Triage 🩺
  Bug

  scverse/scanpy#4406 · Filter by author ChenziqiAdam opened on Oct 8, 2026

• highly_variable_genes(flavor="seurat_v3") flags more than n_top_genes genes when var_names contain duplicates

  Triage 🩺
  Bug

  scverse/scanpy#4405 · Filter by author ChenziqiAdam opened on Oct 8, 2026

• Integration Testing CI Install Failure on python 3.12

  scverse/scanpy#4398 · Filter by author scverse-issue-creator opened on Oct 3, 2026

• Multi-column groupby crashes on non-string observations in dotplot/matrixplot/heatmap

  scverse/scanpy#4384 · Filter by author barlowa124 opened on Sep 28, 2026

• highly_variable_genes with batch_key and subset=True keeps the wrong genes when n_top_genes is not set

  scverse/scanpy#4370 · Filter by author haeganm opened on Sep 17, 2026

• anndata.acc based API for obs_df,var_df

  Area – API
  Enhancement

  scverse/scanpy#4360 · Filter by author flying-sheep opened on Sep 11, 2026

• calculate_qc_metrics(use_raw=True) labels .raw's matrix with adata.var

  scverse/scanpy#4347 · Filter by author Arthur031221 opened on Sep 6, 2026

• The .uns output for scanpy.pp.highly_variable_genes is not documented

  Triage 🩺
  Enhancement

  scverse/scanpy#4341 · Filter by author lazappi opened on Sep 3, 2026

• rank_genes_groups(method="t-test", mean_in_log_space=False) runs the t-test on exponentiated values

  Triage 🩺
  Bug

  scverse/scanpy#4336 · Filter by author cindykrafft opened on Sep 2, 2026

• sc.external.exporting.cellbrowser: cellbrowser_raw_data\sample_colors.tsv does not exist, skipping it An exception has occurred, use %tb to see the full traceback.

  Triage 🩺
  Bug

  scverse/scanpy#4335 · Filter by author danli349 opened on Sep 2, 2026

• anndata.acc replacement for functions taking obsm, layer, …

  Area – API
  Enhancement

  scverse/scanpy#4334 · Filter by author flying-sheep opened on Sep 1, 2026

• sc.pl.paga raises TypeError when cax is passed with multiple colors

  scverse/scanpy#4318 · Filter by author AdvaitS opened on Aug 22, 2026

• Split up rank_genes_groups

  Enhancement

  scverse/scanpy#4305 · Filter by author Intron7 opened on Aug 18, 2026
  2

• Pre 2.0 janitor work

  Area - Documentation 📒Area – Performance 🐌Area – Preprocessing 🧼
  Task

  scverse/scanpy#4286 · Filter by author Zethson opened on Aug 10, 2026
  

• pp.regress_out returns wrong residuals when a covariate barely varies

  Bug

  scverse/scanpy#4280 · Filter by author selmanozleyen opened on Aug 5, 2026
  2

  

• Investigate our neighbors algorithm choice

  Area - Topology 🍩
  Enhancement

  scverse/scanpy#4131 · Filter by author ilan-gold opened on May 19, 2026 · 2.0.0
  15

• wilcoxon DE, vs_all_perturbed

  Enhancement

  scverse/scanpy#4114 · Filter by author zboldyga opened on May 8, 2026
  15

• Investigate networkit (for leiden implementation)

  Enhancement

  scverse/scanpy#4110 · Filter by author ilan-gold opened on May 7, 2026
  4

• Automatically using Dask for large datasets when necessary

  Area - Out of core 💾
  Enhancement

  scverse/scanpy#4095 · Filter by author Zethson opened on Apr 28, 2026
  15

  

• sc.get.aggregate memory leak for Dask array

  Area - Out of core 💾
  Bug

  scverse/scanpy#4074 · Filter by author mumichae opened on Apr 18, 2026
  1

• Add layer parameter to read_10x_* functions

  Area - IO
  Enhancement

  scverse/scanpy#4071 · Filter by author flying-sheep opened on Apr 17, 2026 · 1.13.0
  1

  

• modernize datasets

  Area - Datasets
  Enhancement

  scverse/scanpy#4044 · Filter by author flying-sheep opened on Apr 9, 2026

• Opinionated defaults for 2.0

  Area – API
  Enhancement

  scverse/scanpy#4008 · Filter by author flying-sheep opened on Mar 23, 2026
  5

  

• anndata.acc based API

  Area – API
  Enhancement

  scverse/scanpy#4007 · Filter by author flying-sheep opened on Mar 23, 2026
  5

  

• seaborn is broken with pandas 3: Violin plots squished, points misaligned

  Area - Plotting 🌺Upstream
  Bug

  scverse/scanpy#3991 · Filter by author jaro-slamecka opened on Feb 26, 2026
  2