10 Loupe Browser
Loupe Browser is a desktop application for visualizing 10X Genomics data. Macintosh and Windows versions are available.
We will explore Loupe Browser as an alternative to having to write your own R code.
10.1 Installation
First download Loupe Browser from
https://www.10xgenomics.com/support/software/loupe-browser/downloads
After entering some registration information and agreeing to their privacy policy, click the Download button for your operating system, noting the system requirements. Then follow the installation instructions.
10.2 Tutorial
In this module, we will work through the Loupe Browser online tutorial, starting with the Navigation tutorial.
10.2.1 Load data
Loupe Browser comes with a few sample datasets installed, but we want to load our own data. Use the Linux scp command to download it from the NCGR server. The file is about 328 Mb and may take a few minutes to download. Recall that ‘data’ is a symbolic link to one of the data subdirectories.
scp -P 2309 <user>@inbre.ncgr.org:~/single-cell-workshop/data/aggr-sn_sc.cloupe .