exclude_grey
flag back to doing nothing in the ModuleEigengenes
function because it messed up some downstream tasks, will resolve in a future update.ProjectModules
now excludes modules with too many missing genes in the query dataset, tunable by the overlap_proportion
parameter.MetacellsByGroups
if there are any groups that are excluded by min_cells
.MetacellsByGroups
, instead of the default “RNA”.ModuleEigengenes
takes assay
as an argument, clears up some issues with RunHarmony
.ModuleEigengenes
doesn’t require a “counts” slot to be present in the given assay, but now it throws an error if the normalized data slot is missing.