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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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[pre-commit.ci] pre-commit autoupdate
#278
pre-commit-ci[bot]
closed
5 months ago
0
[pre-commit.ci] pre-commit autoupdate
#277
pre-commit-ci[bot]
closed
6 months ago
0
REL v0.4.9
#276
BorisMuzellec
closed
6 months ago
0
[BUG] UFunc Casting Error when Fitting Dispersions
#275
zaki-bds
closed
6 months ago
4
BUG update genewise dispersions and fitted dispersions of refitted genes
#274
BorisMuzellec
closed
6 months ago
1
[pre-commit.ci] pre-commit autoupdate
#273
pre-commit-ci[bot]
closed
6 months ago
0
Simplify naming convention conversion between pydeseq2 and formulaic
#272
jeandut
opened
6 months ago
0
[BUG] No module named 'pydeseq2.default_inference'
#271
Agamart
closed
6 months ago
2
How to process gene expression data from Affymetrix in Python
#270
abearab
closed
6 months ago
2
[pre-commit.ci] pre-commit autoupdate
#269
pre-commit-ci[bot]
closed
6 months ago
0
fix : enable vst be used "blindly" and to fit its own dispersion
#268
laudmt
closed
5 months ago
4
Add adapt = False (prior_scale=1) option to lfc_shrink()
#267
awalsh17
closed
6 months ago
4
Fix: latex display in sphinx doc
#266
tanguy-marchand
closed
7 months ago
2
[pre-commit.ci] pre-commit autoupdate
#265
pre-commit-ci[bot]
closed
7 months ago
0
support similar apeAdapt argument as in DESeq2::lfcShrink()
#264
awalsh17
closed
6 months ago
2
[BUG] The vst() function does not work when the algorithm switches to a mean-based dispersion trend.
#263
dguin
closed
5 months ago
2
REL 0.4.8
#262
BorisMuzellec
closed
7 months ago
0
[pre-commit.ci] pre-commit autoupdate
#261
pre-commit-ci[bot]
closed
7 months ago
0
BUG add ``continuous_factors`` argument to ``sub_dds``
#260
BorisMuzellec
closed
7 months ago
0
[BUG] tuple index out of range
#259
jsgounot
closed
7 months ago
5
Question (Continuous covariates)/ error with refit_cooks "ValueError: setting an array element with a sequence."
#258
Marwansha
closed
7 months ago
5
[pre-commit.ci] pre-commit autoupdate
#257
pre-commit-ci[bot]
closed
7 months ago
0
chore:upgrading python version
#256
jeandut
closed
7 months ago
1
[BUG] Python3.8 is still listed in documentation and README as being the default but is not supported anymore
#255
jeandut
closed
7 months ago
0
[BUG] Errors saving `DeseqDataSet` to H5AD
#254
jpintar
opened
7 months ago
0
BUG return output with same dimensions as input with mean disp fuction
#253
BorisMuzellec
closed
7 months ago
0
dispersion algorithm
#252
wangjiawen2013
opened
7 months ago
0
[BUG] pydeseq2 v0.4.7 throws IndexError due to anndata awkward variable length array not observed with 0.4.4
#251
dguin
closed
7 months ago
2
[pre-commit.ci] pre-commit autoupdate
#250
pre-commit-ci[bot]
closed
7 months ago
0
[BUG] DE Testing on negative binomial examples
#249
ilan-gold
closed
7 months ago
5
single cell dataset
#248
wangjiawen2013
opened
7 months ago
1
REL bump version
#247
BorisMuzellec
closed
8 months ago
0
BUG fix pvalue adjustment
#246
BorisMuzellec
closed
8 months ago
0
[BUG] All padj is same when independent_filter = False
#245
kgod336336
closed
8 months ago
1
REL bump version
#244
BorisMuzellec
closed
8 months ago
0
BUG fix independent filtering
#243
BorisMuzellec
closed
8 months ago
0
IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed.
#242
lizelx
closed
8 months ago
6
Bug Report: 'n_cpus' and 'n_processes' Keywords Not Recognized in pydeseq2.dds.DeseqDataSet (Version 0.4.4)
#241
chloesavignac
closed
7 months ago
2
REL bump version number
#240
BorisMuzellec
closed
8 months ago
0
BUG Fix new all zero replace
#239
BorisMuzellec
closed
8 months ago
0
Why is replacement not done if it would result in all zero counts?
#238
chubukov
closed
8 months ago
1
[BUG] KeyError in cooks replacement
#237
chubukov
closed
8 months ago
0
MAINT Remove statsmodels
#236
BorisMuzellec
closed
8 months ago
4
Ignore PerfectSeparationWarning
#235
BorisMuzellec
closed
8 months ago
0
ENH implement local fit for trend curve
#234
BorisMuzellec
opened
9 months ago
0
[BUG] Impossible to generate de dds objtect with DeseqDataSet with this update
#233
victorsanchezarevalo
closed
9 months ago
2
[pre-commit.ci] pre-commit autoupdate
#232
pre-commit-ci[bot]
closed
8 months ago
0
[BUG] Negative coefficients in the trend curve
#231
BorisMuzellec
closed
8 months ago
0
[pre-commit.ci] pre-commit autoupdate
#230
pre-commit-ci[bot]
closed
9 months ago
0
CI: ignore the deprecation warning about the future Pyarrow dependency
#229
BorisMuzellec
closed
9 months ago
0
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