Load a single-cell dataset in R

We will now look at our first real scRNA-Seq dataset. In this exercise, you will work on a subset of the dataset allen from the package scRNAseq. The full dataset contains 379 cells from the mouse visual cortex where cells were extracted from different layers of neurons in the visual cortex.

In this exercise, we'll use the function assay() from the package SingleCellExperiment to get the matrix of counts.

The allen object is available for you in your workspace.

Explore the dataset allen.
Create a SingleCellExperiment object via coercion from the dataset allen and assign it to sce. Explore the object sce.
Calculate the total number of reads aligned to each cell using the function colSums(). You can use assay(sce) to get the matrix of counts.

Exercise

Load a single-cell dataset in R

Instructions