Name Mode Size
..
EGSEAclass.R 100755 68 kb
GSCollectionIndexclass.R 100755 11 kb
egseaAux.R 100755 6 kb
egseaMain.R 100755 35 kb
egseaReport.R 100755 16 kb
egseaUtils.R 100755 39 kb
fisher.method.R 100755 2 kb
gsacamera.R 100755 2 kb
gsafry.R 100755 3 kb
gsagage.R 100755 2 kb
gsaglobaltest.R 100755 3 kb
gsagsva.R 100755 4 kb
gsaora.R 100755 4 kb
gsapadog.R 100755 2 kb
gsaplots.R 100755 40 kb
gsaroast.R 100755 2 kb
gsasafe.R 100755 3 kb
htmlUtils.R 100755 30 kb
idxAnno.R 100755 28 kb
wrapperUtils.R 100755 5 kb
README.md
# Ensemble of Gene Set Enrichment Analyses <div align="center"> <img src="inst/logo/EGSEA_logo.png" align="middle" width=250 /> <br /> <sub>Credit: Roberto Bonelli </sub> </div> This package is part of the **Bioconductor** project and implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. **Author:** Monther Alhamdoosh, Luyi Tian, Milica Ng and Matthew Ritchie **Maintainer:** Monther Alhamdoosh <m.hamdoosh at gmail.com> Citation (from within R, enter ```citation("EGSEA")```): Alhamdoosh M, Ng M, Wilson N, Sheridan J, Huynh H, Wilson M and Ritchie M (2017). “Combining multiple tools outperforms individual methods in gene set enrichment analyses.” *Bioinformatics*, 33(3). doi: 10.1093/bioinformatics/btw623. Alhamdoosh M, Law CW, Tian L et al. Easy and efficient ensemble gene set testing with EGSEA [version 1; peer review: 1 approved, 3 approved with reservations]. F1000Research 2017, 6:2010. doi: 10.12688/f1000research.12544.1 # Installation To install the *stable release* of this package, start R and enter: ```{r} ## try http:// if https:// URLs are not supported if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("EGSEA") ``` To install the *development version* of this package, start R and enter: ```{r} install.packages("devtools") # if you have not installed "devtools" package devtools::install_github("malhamdoosh/EGSEA") ``` # Documentation To view documentation for the version of this package installed in your system, start R and enter: ```{r} browseVignettes("EGSEA") ```