Changed factor for normalization of UCell scores, to account for minimal rank. For typical use cases the behaviour is similar to the previous implementation, but has an impact with very large signatures (UCell score distributions are now more homogeneous). See function UCell:::u_stat()) for details.
Add support for Seurat v5 assay and datasets in multiple layers. Added dependency on Seurat >= 5.0.
Change default for chunk.size to 100. On parallelized jobs, this can improve up to 2-fold execution time.
Smaller test dataset (30 cells), to speed up package function checks.
New function SmoothKNN() for k-nearest neighbor smoothing of UCell scores. It can be applied both on SingleCellExperiment and Seurat objects (S3 method).
Add two new vignettes: along with basic usage (vignette 1), there are now dedicated vignettes for running UCell with SingleCellExperiment objects (vignette 2) and Seurat objects (vignette 3). kNN smoothing is illustrated for both object types.
Fixing a bug that prevented storing of feature ranks.
Update code to pass all BioC checks.
The function ScoreSignatures_UCell() and StoreRankings_UCell() accept directly sce objects.
Takes custom BiocParallel::bpparam() object as input to specify parallelisation.
Restructure code to conform to BioC standards.
Switch from future to BiocParallel to parallelize jobs.
Add support for SingleCellExperiment - new function ScoreSignatures_UCell_sce() interacts directly with sce objects.
Signatures cannot be larger than maxRank parameter.
Do not rank more genes (maxRank) than there are in the input matrix.