agedbrain

This repository contains code and files for reproducing the analysis presented in "Neuropathological and transcriptomic characteristics of the aged brain," [LINK/INFO HERE] the platform paper for the Aging, Dementia, and TBI Study.

To reproduce the analysis, do the following:

1. Download everything from the Aging, Dementia, and TBI Study download page (http://aging.brain-map.org/download/index) and save it in the same folder
2. Download this github repository files. Unzip "dataFiles.zip" and save to a folder. Save "TbT_normalization.RData" in the same folder
3. Save the six .r files from this github repository in a different folder
4. Update the top several lines of "Code01_ReadInDataAndFormat.r" with the appropriate folder names (from above)
5. Install the following R packages: sva, WGCNA, gridExtra, ggplot2, gplots, baySeq, edgeR, DESeq, NBPSeq, ROC, and mclust
6. Run the five numbered code files in order

Some useful websites:

1. Allen Institute data portal: http://brain-map.org/
2. The Aging, Dementia, and TBI Study main page: http://aging.brain-map.org/
3. Raw data (FASTQ/bam files) for the RNA-Seq data presented in this study: https://www.niagads.org/datasets/ng00059
4. Link to the open-access eLife article describing this resource: https://elifesciences.org/articles/31126

If you find any errors in this code, please let me know so I can correct them via jeremym@alleninstitute.org. I have validated this code in R version 3.2.5 (2016-04-14), and don't expect other errors, but you never know.