owkin PyDESeq2 issues - Githubissues

owkin / PyDESeq2

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

https://pydeseq2.readthedocs.io/en/latest/

MIT License

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issues

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

#305 maltekuehl opened 3 weeks ago
0
Respect quiet=True in DeseqStats.lfc_shrink

#304 maltekuehl opened 3 weeks ago
0
Random effects

#303 TheAustinator opened 1 month ago
0
[pre-commit.ci] pre-commit autoupdate

#302 pre-commit-ci[bot] opened 1 month ago
0
[pre-commit.ci] pre-commit autoupdate

#301 pre-commit-ci[bot] closed 1 month ago
0
REL v0.4.10

#300 BorisMuzellec closed 1 month ago
0
MAINT cast counts to int when initialising a DeseqDataSet from anndata

#299 BorisMuzellec closed 1 month ago
0
[pre-commit.ci] pre-commit autoupdate

#298 pre-commit-ci[bot] closed 1 month ago
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DOC fix text format in DeseqStats docstring

#297 BorisMuzellec closed 1 month ago
0
BUG: creating columns on all levels even for continuous

#296 umarteauowkin closed 2 months ago
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[pre-commit.ci] pre-commit autoupdate

#295 pre-commit-ci[bot] closed 1 month ago
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DOC: specify what happens if n_cpus and inference are set

#294 umarteauowkin closed 2 months ago
0
Fix Inference n_cpus overwritten issue

#293 yihming closed 2 months ago
1
ENH Remove count DataFrame from calculate_cooks

#292 asistradition closed 1 month ago
3
NANs introduced for some genes, no warning, no error [BUG]

#291 dbdimitrov closed 1 month ago
2
[pre-commit.ci] pre-commit autoupdate

#290 pre-commit-ci[bot] closed 2 months ago
0
CHORE: update code owners

#289 ghost closed 2 months ago
0
Setting different n_cpus in DefaultInference gives results in the same time

#288 yihming closed 2 months ago
4
[BUG] DeseqDataSet.deseq2() still prints when quiet=True is set

#287 yihming opened 2 months ago
4
summary function uses quiet to print

#286 yihming closed 2 months ago
0
[pre-commit.ci] pre-commit autoupdate

#285 pre-commit-ci[bot] closed 2 months ago
0
Poscount implementation & diag(XXT) optimization

#284 asistradition closed 2 months ago
2
[pre-commit.ci] pre-commit autoupdate

#283 pre-commit-ci[bot] closed 3 months ago
0
Replace np.NaN with np.nan -> numpy 2.0 compat

#282 Zethson closed 3 months ago
2
BUG initialize `beta_init` when the design matrix is not full rank

#281 BorisMuzellec closed 3 months ago
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[BUG] local variable 'beta_init' referenced before assignment

#280 redst4r closed 3 months ago
2
[pre-commit.ci] pre-commit autoupdate

#279 pre-commit-ci[bot] closed 3 months ago
0
[pre-commit.ci] pre-commit autoupdate

#278 pre-commit-ci[bot] closed 3 months ago
0
[pre-commit.ci] pre-commit autoupdate

#277 pre-commit-ci[bot] closed 3 months ago
0
REL v0.4.9

#276 BorisMuzellec closed 4 months ago
0
[BUG] UFunc Casting Error when Fitting Dispersions

#275 zaki-bds closed 4 months ago
4
BUG update genewise dispersions and fitted dispersions of refitted genes

#274 BorisMuzellec closed 4 months ago
1
[pre-commit.ci] pre-commit autoupdate

#273 pre-commit-ci[bot] closed 4 months ago
0
Simplify naming convention conversion between pydeseq2 and formulaic

#272 jeandut opened 4 months ago
0
[BUG] No module named 'pydeseq2.default_inference'

#271 Agamart closed 4 months ago
2
How to process gene expression data from Affymetrix in Python

#270 abearab closed 4 months ago
2
[pre-commit.ci] pre-commit autoupdate

#269 pre-commit-ci[bot] closed 4 months ago
0
fix : enable vst be used "blindly" and to fit its own dispersion

#268 laudmt closed 2 months ago
4
Add adapt = False (prior_scale=1) option to lfc_shrink()

#267 awalsh17 closed 4 months ago
4
Fix: latex display in sphinx doc

#266 tanguy-marchand closed 4 months ago
2
[pre-commit.ci] pre-commit autoupdate

#265 pre-commit-ci[bot] closed 4 months ago
0
support similar apeAdapt argument as in DESeq2::lfcShrink()

#264 awalsh17 closed 4 months ago
2
[BUG] The vst() function does not work when the algorithm switches to a mean-based dispersion trend.

#263 dguin closed 2 months ago
2
REL 0.4.8

#262 BorisMuzellec closed 5 months ago
0
[pre-commit.ci] pre-commit autoupdate

#261 pre-commit-ci[bot] closed 5 months ago
0
BUG add ``continuous_factors`` argument to ``sub_dds``

#260 BorisMuzellec closed 5 months ago
0
[BUG] tuple index out of range

#259 jsgounot closed 5 months ago
5
Question (Continuous covariates)/ error with refit_cooks "ValueError: setting an array element with a sequence."

#258 Marwansha closed 5 months ago
5
[pre-commit.ci] pre-commit autoupdate

#257 pre-commit-ci[bot] closed 5 months ago
0
chore:upgrading python version

#256 jeandut closed 5 months ago
1