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

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

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

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

Summary

Version 0.3 introduces a breaking change: using AnnData as a base class for DeseqDataSet, towards the integration of PyDESeq2 to the scverse ecosystem.

What's Changed

• DOC add contribution guidelines by @maikia in #49
• DOC transforming minimal notebook to become example by @maikia in #33
• BENCH remove support for TCGA data by @BorisMuzellec in #54
• DOC add mybinder to examples by @maikia in #55
• DOC improve the "Getting Started" notebook from the example gallery by @BorisMuzellec in #56
• DOC Convert step-by-step notebook to example by @maikia in #58
• BUG Fix add missing joblib_verbosity argument in fit_genewise_dispersions by @BorisMuzellec in #61
• DOC: refactoring by @BorisMuzellec in #59
• DOC Update issue templates: bug by @maikia in #63
• DOC Update issue templates: feat by @maikia in #65
• DOC Community by @maikia in #64
• BUG fix DeseqStats test of dds's replaced attribute by @BorisMuzellec in #62
• DEP removing the notebooksdirectory by @BorisMuzellec in #67
• DOC Moving docs' requirements into the actual docs' requirements file by @mandreux-owkin in #72
• BUG set dds.replaced to False if cohorts don't have enough samples by @BorisMuzellec in #70
• DOC development roadmap by @BorisMuzellec in #24
• CI Basic code coverage by @mandreux-owkin in #74
• TST Unit test for nb_nll by @mandreux-owkin in #75
• CI update workflow by @maikia in #80
• CI add more versions of python to the github workflow by @maikia in #81
• MAIN Adding code owners by @mandreux-owkin in #82
• ENH Anndata integration by @BorisMuzellec in #66
• ENH implement a getter for normalized counts by @BorisMuzellec in #79
• ENH Support type hinting using mypy by @illumination-k in #68
• DOC fix broken RTD example gallery by @BorisMuzellec in #83
• DOC Improve parameter type display by @BorisMuzellec in #87

New Contributors

• @mandreux-owkin made their first contribution in #72
• @illumination-k made their first contribution in #68

Full Changelog: v0.2.1...v0.3

What's Changed

• DOC rearrange home page by @maikia in #31
• ENH Index sorting by @BorisMuzellec in #30
• ENH Paired multi-factor analysis by @BorisMuzellec in #32
• BUG debug DeseqStats constrasts by @BorisMuzellec in #40
• BUG calculate Cooks distances with few samples by @BorisMuzellec in #44
• MAINT remove deprecated _change_lfc_sign attribute of the DeseqStats class by @BorisMuzellec in #47
• BUG raise error when cooks outliers should have been refitted but were not by @BorisMuzellec in #48

Full Changelog: v0.1.1...v0.2.1