This is a script I used to make an R Shiny application that allows for browsing the time-course gene expression signal, and associated statistics, for an experiment where MCF-7 cells were exposed to oxidative stress-inducing compounds. This dataset was published in Free Radical Biology and Medicine, article found here: Levings et al. FRBM. 2021.
I also include the R code (in R Markdown format) used to generate the R data for the app (MCF7-ROS-RNAseq.RData).
To use this app:
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Clone this GitHub repository to [desired location].
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Make sure you have the R programming language and the following packages installed: magrittr, ggplot2, ggrepel, ggtext, gridExtra, scales, shiny, tidyverse, xtable
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Run the following code in your terminal:
R -e "shiny::runApp('[desired location]/MCF7-ROS-RNAseq/app.R')" -
R will run the app, and show what address the plot will be output at. It should look something like:
Listening on http://127.0.0.1:6880 -
Copy the address (eg -
http://127.0.0.1:6880) and paste it into your web browser to use the app.
Raw data sources:
Gene Expression Omnibus (GEO): GSE173664
Shield:
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
