Issues

• pp.combat with a categorical covariate builds a singular design matrix and can leave the batch effect in place

  Triage 🩺
  Bug

  scverse/scanpy#4454 · Filter by author Ghazal-Ghajari opened on Oct 29, 2026
  1

• Dask: highly_variable_genes(flavor="seurat_v3"), calculate_qc_metrics and rank_genes_groups load the whole array into memory

  scverse/scanpy#4445 · Filter by author yangqi-su opened on Oct 27, 2026

• Consider switch to graspologic-native for faster Leiden implementation

  Triage 🩺
  Enhancement

  scverse/scanpy#4441 · Filter by author maltekuehl opened on Oct 26, 2026

• calculate_qc_metrics gives negative pct_counts_in_top_N_genes for sparse int16 X and fails for sparse unsigned integer X

  scverse/scanpy#4440 · Filter by author JoeyTan21 opened on Oct 25, 2026

• Remove louvain

  Task

  scverse/scanpy#4434 · Filter by author flying-sheep opened on Oct 23, 2026
  1

• Remove recipes

  breaking change ‼️
  Task

  scverse/scanpy#4433 · Filter by author flying-sheep opened on Oct 23, 2026
  1

• highly_variable_genes(batch_key=...) selects more than n_top_genes genes (and merges distinct genes) when var_names contain duplicates

  Triage 🩺
  Bug

  scverse/scanpy#4432 · Filter by author ChenziqiAdam opened on Oct 22, 2026

• Integration Testing CI Install Failure on python 3.12

  scverse/scanpy#4425 · Filter by author scverse-issue-creator opened on Oct 20, 2026

• neighbors(method="gauss") returns a non-symmetric connectivity matrix on the sparse (pynndescent / transformer) path

  Triage 🩺
  Bug

  scverse/scanpy#4416 · Filter by author ChenziqiAdam opened on Oct 11, 2026

• highly_variable_genes(flavor="cell_ranger", n_top_genes=n) selects 0 genes when the top genes have infinite normalized dispersion

  Triage 🩺
  Bug

  scverse/scanpy#4415 · Filter by author ChenziqiAdam opened on Oct 11, 2026

• downsample_counts(total_counts=...) on float32 data gives cells/genes more reads than they had once the matrix has > 2^24 counts

  Triage 🩺
  Bug

  scverse/scanpy#4414 · Filter by author ChenziqiAdam opened on Oct 11, 2026

• 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

• 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 and highly_variable_genes

  Enhancement

  scverse/scanpy#4305 · Filter by author Intron7 opened on Aug 18, 2026
  4

• 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