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

v0.3.6

What's Changed

• ENH Introduce quiet attribute to DeseqDataSet that is checked before printing status updates by @noamteyssier in #146
• DOC Add I/O with pandas and pickle tutorial by @BorisMuzellec in #152
• DOC Degrees of freedom corner case by @BorisMuzellec in #153
• ENH Add plotMA() functionality by @emmcauley in #145
• MAINT change clinical variable name to metadata by @BorisMuzellec in #161
• REL set to v0.3.6 by @BorisMuzellec in #162

New Contributors

• @noamteyssier made their first contribution in #146

Full Changelog: v0.3.5...v0.3.6

v0.3.5

What's Changed

• CI runs every week day at 3:30 UTC by @mandreux-owkin in #135
• ENH Add plot_dispersions() by @emmcauley in #137
• DOC add dds.DeseqDataSet.plot_dispersions and utils.make_scatter to… by @BorisMuzellec in #138
• BUG check that save_path is not None before saving in plot_dispersions by @BorisMuzellec in #140
• MAINT turn rank deficiency exception to warning by @BorisMuzellec in #139
• BUG add ref_level argument to sub_dds when refitting cooks outliers by @BorisMuzellec in #143
• REL set to version 0.3.5 by @BorisMuzellec in #144

New Contributors

• @emmcauley made their first contribution in #137

Full Changelog: v0.3.4...v0.3.5

v0.3.4

What's Changed

• BLD remove jupyter from requirements by @BorisMuzellec in #120
• MAINT Expand anndata compatibility by @scottgigante-immunai in #115
• DOC update readthedocs index (n-level factors are supported) by @BorisMuzellec in #126
• BUG fix deseq2_norm bug when applied to a pandas dataframe by @BorisMuzellec in #127
• DOC add bioconda install option to README by @mikecuoco in #129
• ENH Implement fitType="mean" for vst by @scottgigante-immunai in #123
• BUG beta not initialized in irls_solver when the design is not a full rank matrix by @BorisMuzellec in #133
• BUG wrong lfc_shrink sign display by @BorisMuzellec in #131
• REL set version to 0.3.4 by @BorisMuzellec in #134

New Contributors

• @scottgigante-immunai made their first contribution in #119
• @mikecuoco made their first contribution in #129

Full Changelog: v0.3.3...v0.3.4

v0.3.3

What's Changed

• BUG fix slogdet bug due to pandas 2.0 upgrade by @BorisMuzellec in #110
• ENH allow setting the reference level in DeseqDataSet by @BorisMuzellec in #109

Full Changelog: v0.3.2...v0.3.3

v0.3.2

What's Changed

• BUG fix dispersion prior variance by @mikelove in #105
• BUG fix fit_alpha_mle optimization parameterization by @BorisMuzellec in #107

New Contributors

• @mikelove made their first contribution in #105

Full Changelog: v0.3.1...v0.3.2

v0.3.1

What's Changed

• ENH allow initializing a DeseqDataSet from an AnnData object by @BorisMuzellec in #96
• ENH variance stabilizing transformation (VST) by @BorisMuzellec in #99
• ENH multi-level design support by @BorisMuzellec in #101
• BUG fix size factor fitting with zeroes in each gene by @BorisMuzellec in #98
• DOCS add shiny pydeseq2 logo by @BorisMuzellec in #103

Full Changelog: v0.3...v0.3.1