v0.5.0pre1

What's Changed

This version marks a shift towards formulaic designs, i.e. formula like "~condition + treatment", "~condition + condition:treatment", "~condition + exp(cofactor)", etc.

BREAKING CHANGE

python 3.9 is no longer supported.

DeseqDataSet

• Designs should now be provided to DeseqDataSet using the design argument, either in the form of a string representing a formulaic formula (e.g. "~condition + treatment", "~condition + condition:treatment", "~condition + exp(cofactor)"...), or an ndarray directly corresponding to a design matrix.
• design_factors is still supported but throws a DeprecationWarning
• continuous_factors is deprecated, as continuous type inference is handled by formulaic
• ref_level is deprecated
• Due to new decorated methods, DeseqDataSet is no longer picklable. A to_picklable_anndata() method was added to allow users to pickle results for later use.

DeseqStats

• Default contrasts are no longer supported, as they lead to too many errors
• Contrasts may be provided as before for categorical variables (e.g. ["treatment", "test", "control"]), or directly in the form of a contrast vector (a numpy array).
• For now, contrasts for continuous variables are directly specified with a contrast vector.
• lfc_shrink no longer supports a default coef argument

Changelog

• ENH Generic design support using formulaic by @BorisMuzellec in #328
• MAINT Deprecated pandas.DataFrameGroupBy.grouper by @BorisMuzellec in #332

Full Changelog: v0.4.12...v0.5.0pre1

Acknowledgements

@jeandut worked on a first version of formulaic support in #181.
Thanks @grst and @umarteauowkin for your reviews and suggestions!

v0.4.12

What's Changed

• BUG set vst fit type to mean when parametric fails by @BorisMuzellec in #314
• ENH: Memory Optimizations & low_memory Flag by @asistradition in #324

Full Changelog: v0.4.11...v0.4.12

v0.4.11

This version aims to bring support for anndata 0.10.9.

What's Changed

• BUG set varm["replaced"] as a numpy array by @BorisMuzellec in #307
• MAINT Respect quiet=True in DeseqStats.lfc_shrink by @maltekuehl in #304

New Contributors

• @maltekuehl made their first contribution in #304

Full Changelog: v0.4.10...v0.4.11

v0.4.10

What's Changed

• BUG initialize beta_init when the design matrix is not full rank by @BorisMuzellec in #281
• MAINT Replace np.NaN with np.nan -> numpy 2.0 compat by @Zethson in #282
• BUG enable vst be used "blindly" and to fit its own dispersion by @laudmt in #268
• CHORE update code owners by @mandreux-owkin in #289
• MAINT summary function uses quiet to print by @yihming in #286
• ENH Poscount implementation & diag(XXT) optimization by @asistradition in #284
• BUG Inference n_cpus overwritten issue by @yihming in #293
• DOC specify what happens if n_cpus and inference are set by @umarteauowkin in #294
• DOC fix text format in DeseqStats docstring by @BorisMuzellec in #297
• ENH Remove count DataFrame from calculate_cooks by @asistradition in #292
• MAINT cast counts to int when initialising a DeseqDataSet from anndata by @BorisMuzellec in #299

New Contributors

• @Zethson made their first contribution in #282
• @laudmt made their first contribution in #268
• @yihming made their first contribution in #286
• @asistradition made their first contribution in #284
• @umarteauowkin made their first contribution in #294

Full Changelog: v0.4.9...v0.4.10

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