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Issues

Dask support
#2578 · flying-sheep opened on Jul 28, 2023
3

neighbors(method="gauss") returns a non-symmetric connectivity matrix on the sparse (pynndescent / transformer) path
Bug
scverse/scanpy#4416 · 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
Bug
scverse/scanpy#4415 · 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
Bug
scverse/scanpy#4414 · opened on Oct 11, 2026
Integration Testing CI Install Failure on python 3.12
scverse/scanpy#4413 · opened on Oct 11, 2026
Integration Testing CI Test Failure on python 3.14 with prerelease dependencies
scverse/scanpy#4411 · opened on Oct 10, 2026
Integration Testing CI Test Failure on python 3.14
scverse/scanpy#4410 · opened on Oct 10, 2026
downsample_counts(total_counts=...) silently does nothing for Fortran-ordered dense X
Bug
scverse/scanpy#4406 · opened on Oct 8, 2026
highly_variable_genes(flavor="seurat_v3") flags more than n_top_genes genes when var_names contain duplicates
Bug
scverse/scanpy#4405 · opened on Oct 8, 2026
Multi-column groupby crashes on non-string observations in dotplot/matrixplot/heatmap
scverse/scanpy#4384 · 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 · opened on Sep 17, 2026
anndata.acc based API for obs_df,var_df
Enhancement
scverse/scanpy#4360 · opened on Sep 11, 2026
calculate_qc_metrics(use_raw=True) labels .raw's matrix with adata.var
scverse/scanpy#4347 · opened on Sep 6, 2026
The .uns output for scanpy.pp.highly_variable_genes is not documented
Enhancement
scverse/scanpy#4341 · opened on Sep 3, 2026
rank_genes_groups(method="t-test", mean_in_log_space=False) runs the t-test on exponentiated values
Bug
scverse/scanpy#4336 · 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.
Bug
scverse/scanpy#4335 · opened on Sep 2, 2026
anndata.acc replacement for functions taking obsm, layer, …
Enhancement
scverse/scanpy#4334 · opened on Sep 1, 2026
sc.pl.paga raises TypeError when cax is passed with multiple colors
scverse/scanpy#4318 · opened on Aug 22, 2026
Split up rank_genes_groups
Enhancement
scverse/scanpy#4305 · opened on Aug 18, 2026
2
Pre 2.0 janitor work
Task
scverse/scanpy#4286 · opened on Aug 10, 2026
pp.regress_out returns wrong residuals when a covariate barely varies
Bug
scverse/scanpy#4280 · opened on Aug 5, 2026
2
Investigate our neighbors algorithm choice
Enhancement
scverse/scanpy#4131 · opened on May 19, 2026 · 2.0.0
15
wilcoxon DE, vs_all_perturbed
Enhancement
scverse/scanpy#4114 · opened on May 8, 2026
15
Investigate networkit (for leiden implementation)
Enhancement
scverse/scanpy#4110 · opened on May 7, 2026
4
Automatically using Dask for large datasets when necessary
Enhancement
scverse/scanpy#4095 · opened on Apr 28, 2026
15
sc.get.aggregate memory leak for Dask array
Bug
scverse/scanpy#4074 · opened on Apr 18, 2026
1