GSA-Lightning: ultra-fast permutation-based gene set analysis

Billy Heung Wing Chang, Weidong Tian
2016 Bioinformatics  
The computational speed of many gene set analysis methods can be slow due to the computationally demanding permutation step. This article introduces GSA-Lightning, a fast implementation of permutation-based gene set analysis. GSA-Lightning achieves significant speedup compared with existing methods, particularly when the number of gene sets and permutations are large. Availability and implementation: The GSA-Lightning R package is available on Github at https:// github.com/billyhw/GSALightning
more » ... nd on R Bioconductor. The package also contains a comprehensive user's guide with a step-by-step tutorial vignette.
doi:10.1093/bioinformatics/btw349 pmid:27296982 fatcat:dplqkzcwj5gxpbbep53qzg43je