v0.4.9

What's Changed

• DOCS Fix latex display in sphinx doc by @tanguy-marchand in #266
• ENH Add adapt = False (prior_scale=1) option to lfc_shrink() by @awalsh17 in #267
• BUG update genewise dispersions and fitted dispersions of refitted genes by @BorisMuzellec in #274

New Contributors

• @tanguy-marchand made their first contribution in #266
• @awalsh17 made their first contribution in #267

Full Changelog: v0.4.8...v0.4.9

v0.4.8

What's Changed

• MAINT upgrade python version by @jeandut in #256
• BUG return output with same dimensions as input with mean disp fuction by @BorisMuzellec in #253
• BUG add continuous_factors argument to sub_dds by @BorisMuzellec in #260

New Contributors

• @jeandut made their first contribution in #256

Full Changelog: v0.4.7...v0.4.8

v0.4.7

What's Changed

• BUG fix pvalue adjustment by @BorisMuzellec in #246

Full Changelog: v0.4.6...v0.4.7

v0.4.6

What's Changed

• BUG fix independent filtering by @BorisMuzellec in #243

Full Changelog: v0.4.5...v0.4.6

v0.4.5

What's Changed

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

Full Changelog: v0.4.4...v0.4.5

v0.4.4

What's Changed

• BUG Fix min replicates by @BorisMuzellec in #218
• BUG use self._backend instead of 'loky' directly by @adamgayoso in #215

Full Changelog: v0.4.3...v0.4.4

v0.4.3

What's Changed

• MAINT Factor out inference routines by @adamgayoso in #191
• ENH Split vst functions into fit & transform by @hippolyteheuberger in #185
• REL set version 0.4.3 by @BorisMuzellec in #209

New Contributors

• @hippolyteheuberger and @SimonGrouard made their first contribution in #185

Full Changelog: v0.4.2...v0.4.3

v0.4.2

What's Changed

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

New Contributors

• @adamgayoso made their first contribution in #188
• @pre-commit-ci made their first contribution in #193

Full Changelog: v0.4.1...v0.4.2

v0.4.1

What's Changed

• ENH Added lfc null and alt hypothesis in Wald tests by @vcabeli in #172
• MAINT reduce the number of arguments in _fit_rough_dispersions by @BorisMuzellec in #166
• MAINT test against pre-release versions of dependencies by @BorisMuzellec in #171
• REL set release version to 0.4.1 by @BorisMuzellec in #173

New Contributors

• @vcabeli made their first contribution in #172

Full Changelog: v0.4.0...v0.4.1

v0.4.0

What's Changed

PyDESeq2 now supports continuous covariates!

• ENH continuous covariates by @BorisMuzellec in #163
• BUG fix empty old_ref bug caused by split _ by @hermanzhaozzzz in #141

New Contributors

• @hermanzhaozzzz made their first contribution in #141

Full Changelog: v0.3.6...v0.4.0