002‐ Download sample data - rezakj/iCellR GitHub Wiki

• Download and unzip a publicly available sample PBMC scRNA-Seq data.

In R

Set your working directory to the location where you want the file to be downloaded to

setwd("/your/download/directory")

Set the URL of the PBMC 3k dataset as an object

sample.file.url = "https://cf.10xgenomics.com/samples/cell/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz"

Download the file from the URL and save it in your working directory

download.file(url = sample.file.url, 
     destfile = "pbmc3k_filtered_gene_bc_matrices.tar.gz", 
     method = "auto")  

Unzip the downloaded tar.gz file

untar("pbmc3k_filtered_gene_bc_matrices.tar.gz")

# Check the contents of the unzipped folder to ensure successful extraction
list.files()

In your browser

Copy and paste this link in your web browser to download the file and unzip

https://cf.10xgenomics.com/samples/cell/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz