@@ -1,6 +1,6 @@

 Package: celda

 Title: CEllular Latent Dirichlet Allocation

-Version: 1.11.0

+Version: 1.11.1

 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu",

     role = c("aut", "cre")),

     person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")),

@@ -59,19 +59,12 @@ The raw matrix can be passed to the `background` parameter in `decontX` as descr

 We will utilize the 10X PBMC 4K dataset as an example in this vignette. This data can be easily retrieved from the package [TENxPBMCData](http://bioconductor.org/packages/release/data/experiment/html/TENxPBMCData.html). Make sure the the column names are set before running decontX.

 ```{r load_10X, eval=TRUE, message=FALSE}

-# Install TENxPBMCData if is it not already

-if (!requireNamespace("TENxPBMCData", quietly = TRUE)) {

-  if (!requireNamespace("BiocManager", quietly = TRUE)) {

-    install.packages("BiocManager")

-  }

-  BiocManager::install("TENxPBMCData")

-}

-

 # Load PBMC data

 library(TENxPBMCData)

 sce <- TENxPBMCData("pbmc4k")

 colnames(sce) <- paste(sce$Sample, sce$Barcode, sep = "_")

 rownames(sce) <- rowData(sce)$Symbol_TENx

+counts(sce) <- as(counts(sce), "dgCMatrix")

 ```

@@ -59,19 +59,12 @@ The raw matrix can be passed to the `background` parameter in `decontX` as descr

 We will utilize the 10X PBMC 4K dataset as an example in this vignette. This data can be easily retrieved from the package [TENxPBMCData](http://bioconductor.org/packages/release/data/experiment/html/TENxPBMCData.html). Make sure the the column names are set before running decontX.

 ```{r load_10X, eval=TRUE, message=FALSE}

-# Install TENxPBMCData if is it not already

-if (!requireNamespace("TENxPBMCData", quietly = TRUE)) {

-  if (!requireNamespace("BiocManager", quietly = TRUE)) {

-    install.packages("BiocManager")

-  }

-  BiocManager::install("TENxPBMCData")

-}

-

 # Load PBMC data

 library(TENxPBMCData)

 sce <- TENxPBMCData("pbmc4k")

 colnames(sce) <- paste(sce$Sample, sce$Barcode, sep = "_")

 rownames(sce) <- rowData(sce)$Symbol_TENx

+counts(sce) <- as(counts(sce), "dgCMatrix")

 ```