PyDESeq2 Versions Save

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

v0.3.6

10 months ago

What's Changed

ENH Introduce quiet attribute to DeseqDataSet that is checked before printing status updates by @noamteyssier in https://github.com/owkin/PyDESeq2/pull/146
DOC Add I/O with pandas and pickle tutorial by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/152
DOC Degrees of freedom corner case by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/153
ENH Add plotMA() functionality by @emmcauley in https://github.com/owkin/PyDESeq2/pull/145
MAINT change clinical variable name to metadata by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/161
REL set to v0.3.6 by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/162

New Contributors

@noamteyssier made their first contribution in https://github.com/owkin/PyDESeq2/pull/146

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.3.5...v0.3.6

v0.3.5

11 months ago

What's Changed

CI runs every week day at 3:30 UTC by @mandreux-owkin in https://github.com/owkin/PyDESeq2/pull/135
ENH Add plot_dispersions() by @emmcauley in https://github.com/owkin/PyDESeq2/pull/137
DOC add dds.DeseqDataSet.plot_dispersions and utils.make_scatter to… by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/138
BUG check that save_path is not None before saving in plot_dispersions by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/140
MAINT turn rank deficiency exception to warning by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/139
BUG add ref_level argument to sub_dds when refitting cooks outliers by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/143
REL set to version 0.3.5 by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/144

New Contributors

@emmcauley made their first contribution in https://github.com/owkin/PyDESeq2/pull/137

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.3.4...v0.3.5

v0.3.4

1 year ago

What's Changed

BLD remove jupyter from requirements by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/120
MAINT Expand anndata compatibility by @scottgigante-immunai in https://github.com/owkin/PyDESeq2/pull/115
DOC update readthedocs index (n-level factors are supported) by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/126
BUG fix deseq2_norm bug when applied to a pandas dataframe by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/127
DOC add bioconda install option to README by @mikecuoco in https://github.com/owkin/PyDESeq2/pull/129
ENH Implement fitType="mean" for vst by @scottgigante-immunai in https://github.com/owkin/PyDESeq2/pull/123
BUG beta not initialized in irls_solver when the design is not a full rank matrix by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/133
BUG wrong lfc_shrink sign display by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/131
REL set version to 0.3.4 by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/134

New Contributors

@scottgigante-immunai made their first contribution in https://github.com/owkin/PyDESeq2/pull/119
@mikecuoco made their first contribution in https://github.com/owkin/PyDESeq2/pull/129

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.3.3...v0.3.4

v0.3.3

1 year ago

What's Changed

BUG fix slogdet bug due to pandas 2.0 upgrade by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/110
ENH allow setting the reference level in DeseqDataSet by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/109

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.3.2...v0.3.3

v0.3.2

1 year ago

What's Changed

BUG fix dispersion prior variance by @mikelove in https://github.com/owkin/PyDESeq2/pull/105
BUG fix fit_alpha_mle optimization parameterization by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/107

New Contributors

@mikelove made their first contribution in https://github.com/owkin/PyDESeq2/pull/105

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.3.1...v0.3.2

v0.3.1

1 year ago

What's Changed

ENH allow initializing a DeseqDataSet from an AnnData object by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/96
ENH variance stabilizing transformation (VST) by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/99
ENH multi-level design support by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/101
BUG fix size factor fitting with zeroes in each gene by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/98
DOCS add shiny pydeseq2 logo by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/103

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.3...v0.3.1

v0.3

1 year ago

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 https://github.com/owkin/PyDESeq2/pull/49
DOC transforming minimal notebook to become example by @maikia in https://github.com/owkin/PyDESeq2/pull/33
BENCH remove support for TCGA data by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/54
DOC add mybinder to examples by @maikia in https://github.com/owkin/PyDESeq2/pull/55
DOC improve the "Getting Started" notebook from the example gallery by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/56
DOC Convert step-by-step notebook to example by @maikia in https://github.com/owkin/PyDESeq2/pull/58
BUG Fix add missing joblib_verbosity argument in fit_genewise_dispersions by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/61
DOC: refactoring by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/59
DOC Update issue templates: bug by @maikia in https://github.com/owkin/PyDESeq2/pull/63
DOC Update issue templates: feat by @maikia in https://github.com/owkin/PyDESeq2/pull/65
DOC Community by @maikia in https://github.com/owkin/PyDESeq2/pull/64
BUG fix DeseqStats test of dds's replaced attribute by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/62
DEP removing the notebooksdirectory by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/67
DOC Moving docs' requirements into the actual docs' requirements file by @mandreux-owkin in https://github.com/owkin/PyDESeq2/pull/72
BUG set dds.replaced to False if cohorts don't have enough samples by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/70
DOC development roadmap by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/24
CI Basic code coverage by @mandreux-owkin in https://github.com/owkin/PyDESeq2/pull/74
TST Unit test for nb_nll by @mandreux-owkin in https://github.com/owkin/PyDESeq2/pull/75
CI update workflow by @maikia in https://github.com/owkin/PyDESeq2/pull/80
CI add more versions of python to the github workflow by @maikia in https://github.com/owkin/PyDESeq2/pull/81
MAIN Adding code owners by @mandreux-owkin in https://github.com/owkin/PyDESeq2/pull/82
ENH Anndata integration by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/66
ENH implement a getter for normalized counts by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/79
ENH Support type hinting using mypy by @illumination-k in https://github.com/owkin/PyDESeq2/pull/68
DOC fix broken RTD example gallery by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/83
DOC Improve parameter type display by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/87

New Contributors

@mandreux-owkin made their first contribution in https://github.com/owkin/PyDESeq2/pull/72
@illumination-k made their first contribution in https://github.com/owkin/PyDESeq2/pull/68

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.2.1...v0.3

v0.2.1

1 year ago

What's Changed

DOC rearrange home page by @maikia in https://github.com/owkin/PyDESeq2/pull/31
ENH Index sorting by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/30
ENH Paired multi-factor analysis by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/32
BUG debug DeseqStats constrasts by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/40
BUG calculate Cooks distances with few samples by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/44
MAINT remove deprecated _change_lfc_sign attribute of the DeseqStats class by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/47
BUG raise error when cooks outliers should have been refitted but were not by @BorisMuzellec in https://github.com/owkin/PyDESeq2/pull/48

Full Changelog: https://github.com/owkin/PyDESeq2/compare/v0.1.1...v0.2.1

v0.1

1 year ago

v0.1.1

1 year ago