HDBIG-IGEA Documentation

Release 1.0.0, 12/25/2017

© Copyright 2017, ShenLab at Indiana University School of Medicine
Acknowledgements: NIH R01 LM011360 and NSF IIS-1117335.
Contact: Xiaohui Yao (yao2@umai.iu.edu) and/or Li Shen (shenli@iu.edu)
Question or bug reporting: The HDBIG team (hdbig@iu.edu)

1. Introduction

Recent advances in brain imaging and high throughput genotyping and sequencing techniques enable new approaches to study the influence of genetic variation on brain structure and function. HDBIG is a collection of software tools for high dimensional brain imaging genomics. These tools are designed to perform comprehensive joint analysis of heterogeneous imaging genomics data. HDBIG-IGEA is an HDBIG toolkit focusing on high dimensional brain imaging genetics enrichment analysis. The current version includes R implementation of two-dimensional imaging genetic enrichment analysis for identifying high-level imaging genetic associations using enrichment strategy. See below for a list of relevant papers.

· Yao X, Yan J, Kim S, Nho K, Risacher SL, Inlow M, Moore JH, Saykin AJ, Shen L, for the ADNI. (2016) Two-dimensional enrichment analysis for mining high-level imaging genetic associations. Brain Informatics. March 2017, 4(1), pp 27–37. doi: http://dx.doi.org/10.1007/s40708-016-0052-4.

· Yao X, Yan J, Kim S, Nho K, Risacher SL, Inlow M, Moore JH, Saykin AJ, Shen L, for the Alzheimer's Disease Neuroimaging Initiative. (2015) Two-dimensional enrichment analysis for mining high-level imaging genetic associations. BIH 2015: International Conference on Brain Informatics & Health, Lecture Notes in Artificial Intelligence, 9250:115-124, London, UK, 30 August - 2 September, 2015.

2. License

HDBIG-IGEA uses GNU General Public License (GPL). The license description is included in the software package. Please review and accept the license before installing HDBIG-IGEA via any source.

3. Download

Software

· Available at http://www.iu.edu/~hdbig/IGEA

Documentation

· HTML: http://www.iu.edu/~hdbig/IGEA/HDBIG-IGEA-v1.0.0.html

· PDF: http://www.iu.edu/~hdbig/IGEA/HDBIG-IGEA-v1.0.0.pdf

4. Folder Structure and Demo Examples

The package “HDBIG-IGEA-v1.0.0.zip” consists of two subfolders.

· 01_software: The implementation of the two-dimensional imaging genetic enrichment analysis; and an example function and simulated data for demonstrating the code.

· 99_license: The license description.

To test the software, perform the following two steps.

· Launch R, go to “01_software” folder.

· Run “example.R”.