Added the aggregateAcrossGenes() function, to compute an aggregate expression value for gene sets.
Added compute.cohens.d=, compute.delta.mean= and compute.delta.detected= options to scoreMarkers().
Support top=Inf in chooseHighlyVariableGenes().
Also added the bound= argument to set a hard upper/lower bound.
Bugfix for correct filtering with block= in the various filter*QcMetrics() functions when not all blocking levels are present.
Bugfix to clusterKmeans() to respect the user-supplied seed= in relevant initialization methods.
Added a return.graph= option to return the SNN graph from runAllNeighborSteps().
Added a testEnrichment() function for quick and dirty gene set enrichment testing.
Modified runPca() so that it caps number= to the maximum number of available PCs.
Added an analyze() function that provides a one-click approach for analyzing single-cell data.
Added a reportGroupMarkerStatistics() function to combine all marker statistics for a single group into one data frame.