scverse/PyDESeq2

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A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Stars: 761
Forks: 90
Open beginner issues: 0
Indexed issues: 36
Avg merge: 25m
Merged PRs (30d): 10

Dominant language: Python
License: MIT
Last GitHub push: Sep 7, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

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36 open issues indexed

hanging when finding genewise dispersions Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/PyDESeq2#453 · Opened Aug 15, 2026
DeseqStats for a single gene of interest Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

scverse/PyDESeq2#444 · Opened Apr 15, 2026
Stuck at Fitting MAP dispersions... ... done in 0.54 seconds. Open

Difficulty 4/5 3-5 days Newbie friendliness 32/100

scverse/PyDESeq2#433 · 2 comments · Opened Dec 29, 2025
About multifactor analysis Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

scverse/PyDESeq2#418 · Opened Oct 17, 2025
Could data from UCSC Xena used as an input for PyDESeq2? Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

scverse/PyDESeq2#405 · 1 comment · Opened Aug 22, 2025
[BUG] Dispersion estimation fails after 0.4.8 Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/PyDESeq2#391 · 12 comments · 1 reaction · Opened May 27, 2025
Use deres plotting methods Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 30/100

scverse/PyDESeq2#378 · 1 comment · Opened Mar 27, 2025
Simultaneous Batch Correction and DESeq Comparisons between Cell Subsets across Batches Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

scverse/PyDESeq2#376 · 3 comments · Opened Mar 17, 2025
Add instructions on setting a reference level with `formulaic` Open

documentation

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/PyDESeq2#362 · 1 comment · 3 reactions · Opened Jan 24, 2025
Plans to add DESeqDataSetFromTximport? Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/PyDESeq2#359 · 7 comments · 1 reaction · Opened Jan 15, 2025
[BUG] lfc_shrink() generates wrong results Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 30/100

scverse/PyDESeq2#347 · 7 comments · Opened Dec 5, 2024
[BUG] stuck on dds.deseq2() Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/PyDESeq2#338 · 8 comments · Opened Nov 19, 2024
Use `AnnData` as a component rather than a superclass of `DeseqDataSet` Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/PyDESeq2#331 · 3 comments · 2 reactions · Opened Oct 31, 2024
Save / load `DeseqDataSet` states and write anndata to disk as h5ad Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/PyDESeq2#330 · Opened Oct 31, 2024
Feature Request: RLE Plots Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

scverse/PyDESeq2#320 · 2 comments · 1 reaction · Opened Sep 27, 2024
Add support for sample-/gene-dependent normalization factors (e.g., length offsets from pytximport) Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 45/100

scverse/PyDESeq2#305 · 4 comments · 8 reactions · Opened Jul 31, 2024
Random effects Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

scverse/PyDESeq2#303 · 8 reactions · Opened Jul 23, 2024
[BUG] Errors saving `DeseqDataSet` to H5AD Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

scverse/PyDESeq2#254 · 1 reaction · Opened Mar 14, 2024
dispersion algorithm Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

scverse/PyDESeq2#252 · Opened Mar 14, 2024
[BUG] Discrepancies between DESeq2/pyDESeq2 Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/PyDESeq2#217 · 5 comments · 1 reaction · Opened Dec 5, 2023
Different results with the same dependencies Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

scverse/PyDESeq2#216 · 4 comments · Opened Dec 1, 2023
Add a way to create a DeseqDataSet object from normalized count matrix / preprocessed adata object Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/PyDESeq2#205 · 1 comment · Opened Nov 19, 2023
[BUG] Overflows in irls_solver and shape mismatch in _refit_without_outliers when using continuous variable Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/PyDESeq2#201 · Opened Nov 8, 2023
[BUG] Iterative Mode Hangs Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 38/100

scverse/PyDESeq2#198 · 3 comments · 1 reaction · Opened Oct 30, 2023
[RFC] Adding rpy2 (and R and deseq2) as test-only dependency.ies to have more flexible end2end tests Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/PyDESeq2#190 · Opened Oct 19, 2023
[BUG] More flexibility with figures Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

scverse/PyDESeq2#186 · Opened Oct 17, 2023
[FEAT] Add an example with "real data" Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

scverse/PyDESeq2#179 · 2 comments · Opened Oct 17, 2023
Adding LRT test Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/PyDESeq2#176 · 5 comments · 1 reaction · Opened Oct 4, 2023
[BUG] Overflow in `.deseq2()` and and `lfc_shrink()` Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/PyDESeq2#169 · 4 comments · Opened Aug 24, 2023
[Feature request] one vs. all others Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

scverse/PyDESeq2#168 · 8 comments · 10 reactions · Opened Aug 23, 2023
[DOC] Add a tutorial for continuous covariates Open

documentation

Difficulty 3/5 1-2 days Newbie friendliness 55/100

scverse/PyDESeq2#165 · 3 reactions · Opened Aug 8, 2023
fitType = local for vst function Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/PyDESeq2#154 · 3 comments · Opened Jul 19, 2023
[BUG] DeseqDataSet no types given Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 25/100

scverse/PyDESeq2#128 · 2 comments · Opened May 4, 2023
[BUG] Synthetic example dataset doesn't work Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

scverse/PyDESeq2#88 · Opened Feb 26, 2023
Replace `print` to `logging` Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

scverse/PyDESeq2#84 · 1 reaction · Opened Feb 21, 2023
Handling NaN counts Open

enhancement question

Difficulty 4/5 3-5 days Newbie friendliness 35/100

scverse/PyDESeq2#25 · 3 comments · 1 reaction · Opened Dec 28, 2022

scverse/PyDESeq2

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