Skip to content

Issues: owkin/PyDESeq2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

36 Open 101 Closed
36 Open 101 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Update type hints
#343 opened Nov 26, 2024 by BorisMuzellec
Make poscounts accessible from .deseq2() enhancement New feature or request good first issue Good for newcomers
#340 opened Nov 21, 2024 by BorisMuzellec
[BUG] stuck on dds.deseq2() bug Something isn't working
#338 opened Nov 19, 2024 by Erikado4
8
Use AnnData as a component rather than a superclass of DeseqDataSet enhancement New feature or request
#331 opened Oct 31, 2024 by BorisMuzellec
Save / load DeseqDataSet states and write anndata to disk as h5ad enhancement New feature or request
#330 opened Oct 31, 2024 by BorisMuzellec
Use sphinx-autodoc-typehints to fill in type in docstrings documentation Improvements or additions to documentation enhancement New feature or request
#329 opened Oct 31, 2024 by BorisMuzellec
Way to pass lognormalized-regress out expression matrices
#322 opened Oct 5, 2024 by Rafael-Silva-Oliveira
Feature Request: RLE Plots
#320 opened Sep 27, 2024 by jonathjd
2
[BUG] DeseqStats lists a parameter 'n_processes' which it does not accept bug Something isn't working
#310 opened Sep 9, 2024 by cmeesters
Add support for sample-/gene-dependent normalization factors (e.g., length offsets from pytximport)
#305 opened Jul 31, 2024 by maltekuehl
3
Random effects
#303 opened Jul 23, 2024 by TheAustinator
[BUG] DeseqDataSet.deseq2() still prints when quiet=True is set bug Something isn't working
#287 opened Jun 9, 2024 by yihming
@umarteauowkin
4
[BUG] Errors saving DeseqDataSet to H5AD bug Something isn't working
#254 opened Mar 14, 2024 by jpintar
dispersion algorithm
#252 opened Mar 14, 2024 by wangjiawen2013
single cell dataset
#248 opened Mar 12, 2024 by wangjiawen2013
1
[BUG] Discrepancies between DESeq2/pyDESeq2 bug Something isn't working
#217 opened Dec 5, 2023 by ledwmp
4
Different results with the same dependencies
#216 opened Dec 1, 2023 by bernheder
4
Add a way to create a DeseqDataSet object from normalized count matrix / preprocessed adata object enhancement New feature or request
#205 opened Nov 19, 2023 by VictorCurean
1
Option to specify control genes for fitting size factors enhancement New feature or request
#204 opened Nov 15, 2023 by mbernste
[BUG] Overflows in irls_solver and shape mismatch in _refit_without_outliers when using continuous variable bug Something isn't working
#201 opened Nov 8, 2023 by ozanozisik
[BUG] Iterative Mode Hangs bug Something isn't working
#198 opened Oct 30, 2023 by koh-joshua
3
[RFC] Adding rpy2 (and R and deseq2) as test-only dependency.ies to have more flexible end2end tests
#190 opened Oct 19, 2023 by jeandut
[BUG] More flexibility with figures bug Something isn't working
#186 opened Oct 17, 2023 by jbschiratti
Refactor utils.py
#182 opened Oct 17, 2023 by khalilouardini
[FEAT] Add an example with "real data"
#179 opened Oct 17, 2023 by jbschiratti
ProTip! Exclude everything labeled bug with -label:bug.