GSA-Lightning is an R package that provides a fast implementation of permutation-based gene set analysis for two-sample problem. This package is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is necessary for more accurate p-values estimation.
GSA-Lightning requires R 3.3.0 or above (https://www.r-project.org/).
We recommend using the R "devtools" package to install GSALightning from Github.
To install devtools, in an R prompt type:
install.packages("devtools")
To use devtools to install GSA-Lightning, type:
devtools::install_github("billyhw/GSALightning")
Since the package contains some large example gene expression data sets, the download time may take 1-3 minutes. Please kindly be patient.
If the R vignette is also desired, use instead:
library(devtools)
install_github("billyhw/GSALightning", build_vignette = TRUE)
Note the vignette will take some time to build (4-5 minutes) due to some large-scale analysis examples included in the vignette.
The Bioconductor stable release of GSA-Lightning is at:
https://bioconductor.org/packages/release/bioc/html/GSALightning.html
Please consult the R help page of GSA-Lightning for examples:
? GSALight
Billy Heung Wing Chang ([email protected])
Billy Heung Wing Chang and Weidong Tian (2016) GSA-Lightning: Ultra-fast Permutation-based Gene Set Analysis. Bioinformatics. doi: 10.1093/bioinformatics/btw349
http://bioinformatics.oxfordjournals.org/content/early/2016/06/11/bioinformatics.btw349.abstract
GPL (>=2)