General Information
| Description | R package for highly scalable genome-wide association studies using Hadoop clusters |
| Homepage | http://github.com/ibm-bioinformatics/bluesnp |
Publications
BlueSNP: R package for highly scalable genome-wide association studies using Hadoop clusters
Summary:
Computational workloads for genome-wide association studies (GWAS) are growing in scale and complexity outpacing the capabilities of single-threaded software designed for personal computers. The BlueSNP R package implements GWAS statistical tests in the R programming language and executes the calculations across computer clusters configured with Apache Hadoop, a de facto standard framework for distributed data processing using the MapReduce formalism. BlueSNP makes computationally intensive analyses, such as estimating empirical p-values via data permutation, and searching for expression quantitative trait loci over thousands of genes, feasible for large genotype–phenotype datasets.
Availability and implementation:
http://github.com/ibm-bioinformatics/bluesnp
Contact:
rjprill@us.ibm.com
Supplementary information:
Supplementary data are available at Bioinformatics online.
Related Tools
PERMORY
Published July 2010
An LD-exploiting permutation test algorithm for powerful genome-wide association testing
PRIMe
Published March 2011
A method for characterization and evaluation of pleiotropic regions from multiple genome-wide association studies
PERMORY-MPI
Published February 2012
A program for high-speed parallel permutation testing in genome-wide association studies
GRASP
Published June 2014
Analysis of genotype–phenotype results from 1390 genome-wide association studies and corresponding open access database
FAIR Evaluation
Sorry, you must be signed in to evaluate this object.
