NEW FEATURE
plot_gene_express() now has option to add label points with parameter label_points.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
Correct (est_prop/est_prop_test) data usage after changes in v1.1.4
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 use "free_y" axis.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.