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



The GSA-Lightning R package is available on Github at https://github.com/billyhw/GSALightning and on R Bioconductor. The package also contains a comprehensive user's guide with a step-by-step tutorial vignette.



weidong.tian@fudan.edu.cn



Supplementary data are available at Bioinformatics online.
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200436, People's Republic of China Jockey Club School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, Hong Kong SAR.
Billy Heung Wing
BH
Chang
State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200436, People's Republic of China.
Weidong
W
Tian
D000818:Animals; D005796:Genes; D006801:Humans; D012984:Software