@@ -213,7 +213,7 @@ library(Seurat)

 counts <- Read10X("path/to/file")

 # Convert count matrix to SingleCellExperiment to run on decontX

-sce <- SingleCellExperiment(list(counts = counts)). 

+sce <- SingleCellExperiment(list(counts = counts))

 sce <- decontX(sce)

 # Retrieve decontaminated matrix, round to integer, and convert to Seurat object

@@ -222,6 +222,14 @@ decontaminated.counts <- round(decontaminated.matrix)

 seuratObject <- CreateSeuratObject(decontaminated.counts)

 ```

+Conversely, if you have a Seurat object containing raw count matrix and would like to run decontX, simply retrieve the count matrix, convert to SingleCellExperiment, and run on decontX.

+

+```{r seuratIntegration2, eval=FALSE}

+counts <- seurat@assays$RNA@counts

+sce <- SingleCellExperiment(list(counts = counts))

+sce <- decontX(sce)

+```

+

 To import datasets into SingleCellExperiment object, the [singleCellTK](https://bioconductor.org/packages/release/bioc/html/singleCellTK.html) package has several importing functions for different preprocessing tools including CellRanger, STARsolo, BUStools, Optimus, DropEST, SEQC, and Alevin/Salmon. For example, the following code can be used as a template to read in the filtered and raw matrices for multiple samples processed with CellRanger: