All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
- Sync with cookiecutter-template update (version 0.4)
- Bump required Python version to
3.10
- Allow data frames as design matrices
- Allow matrices as input to LEMUR()
- Change example gene to one with clearer differential expression pattern
- Remove error output in `align_harmony
Major rewrite of the API. Instead of adding coefficients as custom fields
to the input AnnData
object, the API now follows an object-oriented style
similar to scikit-learn or SCVI
. This change was motivated by the feedback
during the submission to the scverse
ecosystem.
(Thanks Gregor).
- Instead of calling
fit = pylemur.tl.lemur(adata, ...)
, you now create a LEMUR model (model = pylemur.tl.LEMUR(adata, ...)
) and subsequently callmodel.fit()
,model.align_with_harmony()
, andmodel.predict()
.
- Initial beta release of
pyLemur