calebclass / Shiny-NanoTube

A web app for easier NanoString gene expression analysis

Shiny-NanoTube

Installation

1. Download and install RStudio (and R)
2. Install the NanoTube package from Bioconductor:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("NanoTube")

3. Install other required and recommended libraries.

install.packages(c("shinyBS", "shinyjs", "plotly", "DT"))
BiocManager::install("qusage")

4. Open 'ui.R' in Shiny-NanoTube, and click 'Run'!

A first analysis

1. Download example data sets from the 'data' folder.
2. Run the Shiny-NanoTube app (either from RStudio or the web page).
3. In the Setup tab, load 'GSE132946.zip' in the NanoString data field, and load 'SampleData-GSE132946.csv' in the Sample info table field. A Group Column menu will appear, and open that menu to select 'outcome'.
4. Click the Check Samples button to ensure that the expression data and sample metadata are merged correctly. The 'Filename' and 'name' columns should match.
5. (Optional) Load a gmt file in the Gene set database field.
6. Click Analyze Data.
7. View results in the QC Results, Differential Expression, and Gene Set Analysis (optional) tabs.
8. If you're having trouble, check the Help page, raise an Issue on GitHub, or fill out the form here.