Skip to content

Latest commit

 

History

History
52 lines (36 loc) · 1.38 KB

loupe.md

File metadata and controls

52 lines (36 loc) · 1.38 KB

Loupe Browser 7 allows a user to import seurat objects into its browser framework.
You can use majority of features of the Loupe Browser in the Loupe browser GUI. It can be a great resource to visualize marker genes/ custom gene lists in an interactive way.


Getting Started:

To get started, please install the loupeR package using the following code chunk:

remotes::install_github("10XGenomics/loupeR")
loupeR::setup()

Once installed, please load the loupeR library and follow the following steps.

# import the library
library("loupeR")

First we will extract the assay of interest and save it to a variable

# Gene Expression RNA assay, if working with SCT, please change the "RNA" to "SCT"
assay <- seurat_obj[["RNA"]]

Next we isolate the count data from the assay object that we just created.

# get counts matrix from either the old or newer formats of assay
counts <- counts_matrix_from_assay(assay)

Lastly, we will use the create_loupe function to create a loupe file named mySeuratObject.cloupe

# convert the count matrix, clusters, and projections into a Loupe file
create_loupe(
    counts,
    clusters = select_clusters(seurat_obj),
    projections = select_projections(seurat_obj),
    output_name = "mySeuratObject"
)

Once finished, open up the loupe browser and upload the mySeuratObject.cloupe file.

Happy Exploring!!!