Cell Ranger DNA 1.0 (latest), printed on 03/23/2019
Loupe scDNA Browser is a genome browser specifically designed to assist with analysis of single cell CNV data. We will first take a quick tour of the Loupe scDNA Browser user interface and navigation controls.
Upon loading the MKN-45 Tutorial dataset, you will see the following screen:
And here is that same screen with the main components labeled:
Conceptually, Loupe scDNA Browser presents the copy number and heterogeneity of a subtree of nodes rooted at a single group or cell in the hierarchy. The heatmap displays copy number or heterogeneity, as well as legends for color and the currently visible genomic region. The tree panel shows the currently visible subtree, and allows you to descend down the tree to investigate different nodes. The trace shows aggregate information about the current root node. Finally, the navigation panel allows you to ascend the tree hierarchy, change the visible genomic region, export data, and change visual settings.
Let us give some names to the main interactive elements of Loupe scDNA Browser. Feel free to refer back to this diagram for names of elements when they are mentioned in subsequent sections.
Now, let us start exploring the data.