UCell version 2.10

UCell for Bioconductor 3.20

UCell version 2.8

New in this release (Bioconductor 3.19):

• Add support for multi-layer objects in Seurat v5. 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.

UCell version 2.6

New in this release (Bioconductor 3.18):

• Addresses compatibility with Seurat v5 assays
• Updated implementation of nearest neighbor weighting for SmoothKNN(): neighbor cells are weighted by $(1-decay)^n$, where n is the n-th neighbor and decay is a tunable parameter between 0 and 1.

UCell version 2.4

New in this release (Bioconductor 3.17):

• Enables SmoothKNN directly on gene expression slots. By specifying the list of genes to smooth and the desired assay, it creates a new assay (given by assay . suffix) with the knn-smoothed gene expression values. See the vignettes for examples.
• Improved handling of break cases where object contains 0 or 1 cell.

UCell version 2.2

New in this release (Bioconductor 3.16):

• 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.

UCell version 2.0

New in this version:

• UCell is now on Bioconductor. Install with: BiocManager::install("UCell")
• Improved interoperability with SingleCellExperiment objects
• Takes an optional BiocParallel::bpparam() object as input to customize parallelisation.

UCell version 1.3

New in this release:

• Switch from future to BiocParallel to parallelize jobs (towards BioC submission)
• Add support for SingleCellExperiment - function ScoreSignatures_UCell() 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

UCell version 1.1

New in version 1.1.0:

You can now specify positive and negative gene sets in signatures. For example, build signatures as:

markers <- list()
markers$Tcell_gd <- c("TRDC+", "TRGC1+", "TRGC2+", "TRDV1+","TRAC-","TRBC1-","TRBC2-")
markers$Tcell_NK <- c("FGFBP2+", "SPON2+", "KLRF1+", "FCGR3A+", "CD3E-","CD3G-")
markers$Tcell_CD4 <- c("CD4","CD40LG")
markers$Tcell_CD8 <- c("CD8A","CD8B")
markers$Tcell_Treg <- c("FOXP3","IL2RA")

If you don't specify +/- after a gene name, it is assumed to be part of the positive gene set.

The UCell score is calculated as: U = max(0, U⁺ - w_neg * U^-)

where U⁺ and U^- are respectively the U scores for the positive and negative set, and w_neg is a weight on the negative set.

When no negative set of genes is present, U^- = 0 and U = U⁺, therefore the behavior is identical to previous UCell versions.

UCell version 1.0

First stable release of UCell