Code and files for reproducing the analysis presented in "Neuropathological and transcriptomic characteristics of the aged brain," the platform paper for the Aging, Dementia, and TBI Study.
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
CONTRIBUTING.md
Code01_ReadInDataAndFormat.r
Code02_RenormalizeRNASeqData.r
Code03_Pathology_Figures_1a_2_3a_4c.r
Code04_WGCNAIdentifiesInflammationAndTau_Figure_3bc_4bd.r
Code05_GeneExpressionVsDementiaAndRIN_Figure_4a_5.r
LICENSE
README.md
TbT_normalization.RData
dataFiles.zip
mdmr_r.beta.1.0.1.r

README.md

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: [Not yet available]

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.