PyDESeq2 Versions Save

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

v0.4.9

2 weeks ago

What's Changed

DOCS Fix latex display in sphinx doc by @tanguy-marchand in https://github.com/owkin/PyDESeq2/pull/266
ENH Add adapt = False (prior_scale=1) option to lfc_shrink() by @awalsh17 in https://github.com/owkin/PyDESeq2/pull/267
BUG update genewise dispersions and fitted dispersions of refitted genes by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/274

New Contributors

@tanguy-marchand made their first contribution in https://github.com/owkin/PyDESeq2/pull/266
@awalsh17 made their first contribution in https://github.com/owkin/PyDESeq2/pull/267

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.4.8...v0.4.9

v0.4.8

1 month ago

What's Changed

MAINT upgrade python version by @jeandut in https://github.com/owkin/PyDESeq2/pull/256
BUG return output with same dimensions as input with mean disp fuction by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/253
BUG add continuous_factors argument to sub_dds by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/260

New Contributors

@jeandut made their first contribution in https://github.com/owkin/PyDESeq2/pull/256

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.4.7...v0.4.8

v0.4.7

2 months ago

What's Changed

BUG fix pvalue adjustment by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/246

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.4.6...v0.4.7

v0.4.6

2 months ago

What's Changed

BUG fix independent filtering by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/243

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.4.5...v0.4.6

v0.4.5

2 months ago

What's Changed

MAINT Add back n_cpus argument in DeseqDataSet by @vcabeli in https://github.com/owkin/PyDESeq2/pull/226
MAINT Remove statsmodels by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/236
BUG Fix new all zero replace by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/239
TST ignore the DeprecationWarning from pandas is_categorical_dtype by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/223
DOC update sphinx requirements by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/228
CI ignore the deprecation warning about the future Pyarrow dependency by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/229
REL bump version number by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/240

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.4.4...v0.4.5

v0.4.4

5 months ago

What's Changed

BUG Fix min replicates by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/218
BUG use self._backend instead of 'loky' directly by @adamgayoso in https://github.com/owkin/PyDESeq2/pull/215

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.4.3...v0.4.4

v0.4.3

5 months ago

What's Changed

MAINT Factor out inference routines by @adamgayoso in https://github.com/owkin/PyDESeq2/pull/191
ENH Split vst functions into fit & transform by @hippolyteheuberger in https://github.com/owkin/PyDESeq2/pull/185
REL set version 0.4.3 by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/209

New Contributors

@hippolyteheuberger and @SimonGrouard made their first contribution in https://github.com/owkin/PyDESeq2/pull/185

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.4.2...v0.4.3

v0.4.2

5 months ago

What's Changed

BUG division by zero when num_samples == num_vars by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/175
MAINT Drop iPython dependency and simple print instead by @adamgayoso in https://github.com/owkin/PyDESeq2/pull/188
CI Add ruff pre-commit hook by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/192
CI Remove precommit from workflow by @adamgayoso in https://github.com/owkin/PyDESeq2/pull/195
CI remove test_docstrings (duplicate with ruff, which runs pydocstyle) by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/196
DOC update frontpage with latest features and Bioinformatics paper ref by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/200
BUG set normed_counts in sub_dds before recomputing genewise dispersions when refitting by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/207

New Contributors

@adamgayoso made their first contribution in https://github.com/owkin/PyDESeq2/pull/188
@pre-commit-ci made their first contribution in https://github.com/owkin/PyDESeq2/pull/193

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.4.1...v0.4.2

v0.4.1

7 months ago

What's Changed

ENH Added lfc null and alt hypothesis in Wald tests by @vcabeli in https://github.com/owkin/PyDESeq2/pull/172
MAINT reduce the number of arguments in _fit_rough_dispersions by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/166
MAINT test against pre-release versions of dependencies by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/171
REL set release version to 0.4.1 by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/173

New Contributors

@vcabeli made their first contribution in https://github.com/owkin/PyDESeq2/pull/172

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.4.0...v0.4.1

v0.4.0

9 months ago

What's Changed

PyDESeq2 now supports continuous covariates!

ENH continuous covariates by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/163
BUG fix empty old_ref bug caused by split _ by @hermanzhaozzzz in https://github.com/owkin/PyDESeq2/pull/141

New Contributors

@hermanzhaozzzz made their first contribution in https://github.com/owkin/PyDESeq2/pull/141

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.3.6...v0.4.0