Releases: owkin/PyDESeq2
Releases · owkin/PyDESeq2
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
v0.3.0
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 infit_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
'sreplaced
attribute by @BorisMuzellec in #62 - DEP removing the
notebooks
directory by @BorisMuzellec in #67 - DOC Moving docs' requirements into the actual docs' requirements file by @mandreux-owkin in #72
- BUG set
dds.replaced
toFalse
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
PyDESeq2 0.2.1
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 theDeseqStats
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
v0.1.1
change version to 0.1.1 for release
v0.1
v0.1