Issues

• Integration Testing CI Install Failure on python 3.12

  scverse/PyDESeq2#478 · Filter by author scverse-issue-creator opened on Oct 15, 2026

• Integration Testing CI Test Failure on python 3.14 with prerelease dependencies

  scverse/PyDESeq2#476 · Filter by author scverse-issue-creator opened on Oct 1, 2026

• hanging when finding genewise dispersions

  bug
  scverse/PyDESeq2#453 · Filter by author Dillon214 opened on Aug 15, 2026

• DeseqStats for a single gene of interest

  scverse/PyDESeq2#444 · Filter by author Marwansha opened on Apr 15, 2026
  1

• Stuck at Fitting MAP dispersions... ... done in 0.54 seconds.

  scverse/PyDESeq2#433 · Filter by author xin4396 opened on Dec 29, 2025
  2

• About multifactor analysis

  scverse/PyDESeq2#418 · Filter by author hfl112 opened on Oct 17, 2025

• Could data from UCSC Xena used as an input for PyDESeq2?

  scverse/PyDESeq2#405 · Filter by author fredsamhaak opened on Aug 22, 2025
  1

• [BUG] Dispersion estimation fails after 0.4.8

  bug
  scverse/PyDESeq2#391 · Filter by author gennadyFauna opened on May 27, 2025
  12

• Use deres plotting methods

  enhancement
  scverse/PyDESeq2#378 · Filter by author BorisMuzellec opened on Mar 27, 2025
  1

• Simultaneous Batch Correction and DESeq Comparisons between Cell Subsets across Batches

  scverse/PyDESeq2#376 · Filter by author Willt1128 opened on Mar 17, 2025
  3

• Add instructions on setting a reference level with formulaic

  documentation
  scverse/PyDESeq2#362 · Filter by author BorisMuzellec opened on Jan 24, 2025
  2

• Plans to add DESeqDataSetFromTximport?

  scverse/PyDESeq2#359 · Filter by author annegreuBI opened on Jan 15, 2025
  7

• [BUG] lfc_shrink() generates wrong results

  bug
  scverse/PyDESeq2#347 · Filter by author martinPasen opened on Dec 5, 2024
  7

• [BUG] stuck on dds.deseq2()

  bug
  scverse/PyDESeq2#338 · Filter by author Erikado4 opened on Nov 19, 2024
  8

• Use AnnData as a component rather than a superclass of DeseqDataSet

  enhancement
  scverse/PyDESeq2#331 · Filter by author BorisMuzellec opened on Oct 31, 2024
  3

• Save / load DeseqDataSet states and write anndata to disk as h5ad

  enhancement
  scverse/PyDESeq2#330 · Filter by author BorisMuzellec opened on Oct 31, 2024

• Feature Request: RLE Plots

  scverse/PyDESeq2#320 · Filter by author jonathjd opened on Sep 27, 2024
  2

• Add support for sample-/gene-dependent normalization factors (e.g., length offsets from pytximport)

  enhancement
  scverse/PyDESeq2#305 · Filter by author maltekuehl opened on Jul 31, 2024
  4

• Random effects

  scverse/PyDESeq2#303 · Filter by author TheAustinator opened on Jul 23, 2024

• [BUG] Errors saving DeseqDataSet to H5AD

  bug
  scverse/PyDESeq2#254 · Filter by author jpintar opened on Mar 14, 2024

• dispersion algorithm

  scverse/PyDESeq2#252 · Filter by author wangjiawen2013 opened on Mar 14, 2024

• [BUG] Discrepancies between DESeq2/pyDESeq2

  bug
  scverse/PyDESeq2#217 · Filter by author ledwmp opened on Dec 5, 2023
  5

• Different results with the same dependencies

  scverse/PyDESeq2#216 · Filter by author bernheder opened on Dec 1, 2023
  4

• Add a way to create a DeseqDataSet object from normalized count matrix / preprocessed adata object

  enhancement
  scverse/PyDESeq2#205 · Filter by author VictorCurean opened on Nov 19, 2023
  1

• [BUG] Overflows in irls_solver and shape mismatch in _refit_without_outliers when using continuous variable

  bug
  scverse/PyDESeq2#201 · Filter by author ozanozisik opened on Nov 8, 2023