NEWS.md
NEW FEATURES
findMarkers_1vAll() now only returns standardized log fold-change values, which cuts default run time roughly in half. A new parameter raw_logFC has been added; when TRUE, it yields the old behavior of returning both versions of the log fold-change.findMarkers_1vAll() can now be parallelized with near-linear speedup via a new BPPARAM parameter.NEW FEATURES
get_mean_ratio() has a new BPPARAM parameter allowing parallelization. Run time without parallelization was also marginally improved.BUG FIXES
Package BisqueRNA is no longer a suggested dependency (no longer available on CRAN).
Vignette “Deconvolution Benchmark in Human DLPFC” now loads pre-computed est_prop data instead of running Bisque deconvolution.
NEW FEATURES
plot_gene_express() now has the option to change plot_type to ‘violin’ or ‘boxplot’BUG FIXES
get_mean_ratio() was initially coercing sparse matrices into in memory matrices. We resolved this by using MatrixGenerics::rowMeans() and MatrixGenerics::rowMedians(). This issue was reported by @cyntsc.NEW FEATURES
DeconvoBuddies that introduces the Mean Ratio method for identifying cluster marker genes as implemented in get_mean_ratio(). This method is described in more detail at https://doi.org/10.1101/2024.02.09.579665. This package also provides a wrapper to scran::findMarkers() for identifying marker genes expressed in one cluster compared to all remaining ones. See findMarkeres_1vAll() for more details. Additionally, DeconvoBuddies provides plotting functions for visualizing gene expression as violin plots across different clusters. These plots are much smaller in size compared to other ones you can make with scater::plotExpression(). See plot_gene_express(), plot_marker_express(), and related functions.