runGRaNIE() that relate to the (experimental) GC correction features that GRaNIE offers to enable fine-tuning GC correction.runGRaNIE
WNN_knn from prepareSeuratData_GRaNIE(), non default values are now properly propagatedrecalculateVariableFeatures from prepareSeuratData_GRaNIE(), now setting to all works (again)prepareSeuratData_GRaNIE(). It is now (again) possible to cluster by an existing metavariable.minCellsPerCluster in prepareSeuratData_GRaNIE(): 100 instead of 25. Note that this changes results for previous workflows when this parameter is not explicitly specified.cellTypeAnnotationCol for prepareSeuratData_GRaNIE()
'RNA' not found in this Seurat object that was introduced in a 0.3.0 when the RNA assay was not called RNA.prepareSeuratData_GRaNIE() became a significant update, with clearer (and more) arguments. It is now possible to provide pre-normalized RNA data. In addition, additional parameters related to the LSI normalization for ATAC as well as parameters related to dimensionality reduction can now be specified.compareConnections_upsetPlots(). This function takes a list of GRaNIE eGRNs and produces a summary upset plot to compare among all input eGRNs. It can be used for TF-peak, TF-gene, TF-peak-gene and peak-gene pairs.corMethod to the GRaNIE batch function and the wrapper to allow overriding and specifying the correlation methodprepareSeuratData_GRaNIE() that appeared sometimes when using a custom pseudobulk variable as source for clustering. Thanks to Gerard for noticing and fixing!