issues
search
owkin
/
PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
https://pydeseq2.readthedocs.io/en/latest/
MIT License
584
stars
62
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
DOC update sphinx requirements
#228
BorisMuzellec
closed
9 months ago
0
[pre-commit.ci] pre-commit autoupdate
#227
pre-commit-ci[bot]
closed
9 months ago
0
Add back n_cpus argument in DeseqDataSet
#226
vcabeli
closed
9 months ago
1
[pre-commit.ci] pre-commit autoupdate
#225
pre-commit-ci[bot]
closed
9 months ago
0
[BUG] error when running lfc_shrink
#224
Joey-Xue
closed
9 months ago
3
TST: ignore the DeprecationWarning from pandas `is_categorical_dtype`
#223
BorisMuzellec
closed
10 months ago
0
[pre-commit.ci] pre-commit autoupdate
#222
pre-commit-ci[bot]
closed
10 months ago
0
[pre-commit.ci] pre-commit autoupdate
#221
pre-commit-ci[bot]
closed
10 months ago
0
[pre-commit.ci] pre-commit autoupdate
#220
pre-commit-ci[bot]
closed
10 months ago
0
REL set version 0.4.4
#219
BorisMuzellec
closed
10 months ago
0
BUG Fix min replicates
#218
BorisMuzellec
closed
10 months ago
0
[BUG] Discrepancies between DESeq2/pyDESeq2
#217
ledwmp
opened
10 months ago
4
Different results with the same dependencies
#216
bernheder
opened
11 months ago
4
[bugfix] use self._backend instead of 'loky' directly
#215
adamgayoso
closed
11 months ago
0
Easier access to `n_cpus` argument in `DeseqDataSet`
#214
BorisMuzellec
closed
9 months ago
0
Support for arbitratry design matrices and contrast vectors
#213
grst
opened
11 months ago
7
Batch Effect Normalisation for DEG study
#212
rsmashon
closed
8 months ago
2
[pre-commit.ci] pre-commit autoupdate
#211
pre-commit-ci[bot]
closed
11 months ago
0
Using data from Kallisto
#210
PelFritz
closed
8 months ago
2
REL set version 0.4.3
#209
BorisMuzellec
closed
11 months ago
0
REL set version 0.4.2
#208
BorisMuzellec
closed
11 months ago
0
BUG set normed_counts in sub_dds before recomputing genewise dispersions when refitting
#207
BorisMuzellec
closed
11 months ago
0
[pre-commit.ci] pre-commit autoupdate
#206
pre-commit-ci[bot]
closed
11 months ago
0
Add a way to create a DeseqDataSet object from normalized count matrix / preprocessed adata object
#205
VictorCurean
opened
11 months ago
1
Option to specify control genes for fitting size factors
#204
mbernste
opened
11 months ago
0
[pre-commit.ci] pre-commit autoupdate
#203
pre-commit-ci[bot]
closed
11 months ago
0
Explanation of ref_level argument of DeseqDataSet() in the tutorials
#202
ozanozisik
opened
11 months ago
0
[BUG] Overflows in irls_solver and shape mismatch in _refit_without_outliers when using continuous variable
#201
ozanozisik
opened
11 months ago
0
DOC update frontpage with latest features and Bioinformatics paper ref
#200
BorisMuzellec
closed
11 months ago
0
[pre-commit.ci] pre-commit autoupdate
#199
pre-commit-ci[bot]
closed
11 months ago
0
[BUG] Iterative Mode Hangs
#198
koh-joshua
opened
1 year ago
3
[pre-commit.ci] pre-commit autoupdate
#197
pre-commit-ci[bot]
closed
12 months ago
0
CI remove test_docstrings (duplicate with ruff, which runs pydocstyle)
#196
BorisMuzellec
closed
1 year ago
0
Remove precommit from workflow
#195
adamgayoso
closed
1 year ago
0
DeseqDataSet on Normalized Counts
#194
dstrib
closed
11 months ago
4
[pre-commit.ci] pre-commit autoupdate
#193
pre-commit-ci[bot]
closed
1 year ago
0
CI: Add ruff pre-commit hook
#192
BorisMuzellec
closed
1 year ago
3
Factor out inference routines
#191
adamgayoso
closed
11 months ago
5
[RFC] Adding rpy2 (and R and deseq2) as test-only dependency.ies to have more flexible end2end tests
#190
jeandut
opened
1 year ago
0
_refit_without_outliers raise design matrix is not full rank error
#189
michelegentili93
closed
1 year ago
1
Drop iPython dependency and simple print instead
#188
adamgayoso
closed
1 year ago
0
Factoring out the core implementation with a `DESeqImplementation` class
#187
adamgayoso
closed
11 months ago
3
[BUG] More flexibility with figures
#186
jbschiratti
opened
1 year ago
0
Split vst functions into fit & transform
#185
hippolyteheuberger
closed
11 months ago
2
[Enhancement] `expanded` argument not used in `utils.build_design_matrix`
#184
khalilouardini
opened
1 year ago
0
Tutorial including interactions terms in the design
#183
khalilouardini
opened
1 year ago
0
Refactor `utils.py`
#182
khalilouardini
opened
1 year ago
0
Adding interaction terms to the design matrix
#181
khalilouardini
closed
11 hours ago
22
Adding an example with real data
#180
jbschiratti
opened
1 year ago
0
[FEAT] Add an example with "real data"
#179
jbschiratti
opened
1 year ago
0
Previous
Next