SeurSelect

SeuSelect is a tool to make cell selections from a scRNA-seq experiment via a Seurat object. It is a Shiny based application.

Discover a demo on shinyapp.io

Demo

Installation

library(devtools)
install_github("GhislainFievet/SeurSelect")

and load the library

library(seurselect)

Basic use

You need a Seurat object, let's say pbmc.
You can get a Seurat object example:

download.file("https://www.dropbox.com/s/0xbzyfpr3eruapu/pbmc.RData?raw=1","pbmc.RData")
load("pbmc.RData")
pbmc

To run the app execute:

my.selections = SeurSelect(pmbc)

On application exit, cell selections are stored in my.selections variable.

Use case example

In this example from the demo we show how to select and export cells from the Seurat VlnPlot.

1. Click create a selection
   To create a new selection click on the create a selection button.
   
2. Select the VlnPlot tab
   You can make a selection from 4 different Seurat plots:

• DimPlot
• FeatureScatter
• VlnPlot
• Featureplot
  

3. Select the gene and the metadata to display on the plot, and click OK
   We want to select the CD4+ from the T cell group so we choose gene = CD4 and metadata = human_clusters.
   
4. Select from the interactive plot
   With the select tool you can select the cells you want, here the CD4+ from the T cells type. You can see the selected cells on the right plot.
   
5. Click save selection to store the list on the table.
   Provide a name, a description (optional) and click OK to add the selection on the list.
   
6. The selection is added to the selection table.
   
7. Click on Back to console button to exit the application.
   On application exit, cells selections are stored in the variable my.selections