braindex: brain developmental expression portal

About

This repository hosts the code for a directory of shiny apps created to visualize and interrogate brain developmental gene expression data. Each app is designed for a different type of data.

Directory organization

In this directory, several resources pertain globally to the portal:

• www: Special directory to expose resources for the website, including the CSS specification for the index page and individual apps, the portal and lab logos
• www/layout: Files containing the HTML for various page parts (e.g. header, footer) inserted into each app for custom styling and navigation, using the helper functions in www/ui_functions.R
• index.html: Contains the HTML for the homepage, which links to the apps hosted in the directory
• style.R: An R script which can be sourced by each app, containing styles shared across apps. Currently contains a ggplot2 theme, theme_min().

There is one directory for each app, containing at minimum two R files server.R and ui.R, and a data directory data.

• lifespan: Containts the R code for the shiny app for exploring gene expression in the brain across the lifespan, based on data from the BrainSpan project
• clusters: Contains the R code for the shiny app for exploring gene expression based on clusters from the scRNAseq atlas of the developing mouse forebrain and pons generated by our lab

Datasets which can be explored with the app

• Miller, J.A. et al. (2014) Transcriptional landscape of the prenatal human brain, Nature 508: 199-206. doi:10.1038/nature13185 (Data is © 2010 Allen Institute for Brain Science. Allen Human Brain Atlas. Available from: https://www.brainspan.org/)

• Jessa, S. et al. (2019) Stalled developmental programs at the root of pediatric brain tumors, Nature Genetics 51: 1702-1713. doi:10.1038/s41588-019-0531-7