@@ -44,7 +44,7 @@ exportSCEtoAnnData <- function(sce,

             "If one of these have been previously run to install the modules,",

             "make sure to run selectSCTKConda() or selectSCTKVirtualEnvironment(),",

             " respectively, if R has been restarted since the module installation.",

-            " Alternatively, Scrublet can be installed on the local machine",

+            " Alternatively, 'scanpy' can be installed on the local machine",

             "with pip (e.g. pip install --user scanpy) and then the 'use_python()'",

             " function from the 'reticulate' package can be used to select the",

             " correct Python environment.")

@@ -68,7 +68,8 @@ runScDblFinder <- function(inSCE,

                             samples = sample,

                             artificialDoublets = simDoublets,

                             k = nNeighbors,

-                            verbose = FALSE

+                            verbose = FALSE,

+                            BPPARAM = BPPARAM

                             ))

   if(length(rm.ix) > 0){

     inSCE <- mergeSCEColData(inSCE1 = inSCEOrig, inSCE2 = inSCE)

@@ -1069,7 +1069,7 @@ convertSCEToSeurat <- function(inSCE, countsAssay = NULL, normAssay = NULL,

   if (length(SingleCellExperiment::reducedDims(inSCE)) > 0 && copyReducedDim) {

     for (redc in SingleCellExperiment::reducedDimNames(inSCE)) {

       reDim <- SingleCellExperiment::reducedDim(inSCE, redc)

-      colnames(reDim) <- paste0(redc, "_", seq_len(length(colnames(reDim))))

+      colnames(reDim) <- paste0(redc, "_", seq_len(ncol(reDim))) #length(colnames(reDim)))

       rownames(reDim) <- gsub('_', '-', rownames(reDim))

       key <-  gsub('_', '', redc)

       seuratObject@reductions[[redc]] <- Seurat::CreateDimReducObject(embeddings = reDim,