rapidGSEA: Speeding up gene set enrichment analysis on multi-core CPUs and CUDA-enabled GPUs.

Christian HundtAndreas HildebrandtBertil Schmidt

Published in: BMC bioinformatics (2016)

cudaGSEA outperforms broadGSEA by around two orders-of-magnitude on a single Tesla K40c or GeForce Titan X GPU. ompGSEA provides around one order-of-magnitude speedup to broadGSEA on a standard Xeon CPU. The rapidGSEA suite is open-source software and can be downloaded at https://github.com/gravitino/cudaGSEA as standalone application or package for the R framework.

Keyphrases

magnetic resonance
copy number
genome wide
data analysis
gene expression
dna methylation