allenaigit/pathwayko: PathwayKO: An R package for knock-out pathway enrichment analysis

PathwayKO is an R package for knock-out pathway enrichment analysis, excavating the true positive KO KEGG pathways that contain and are impacted by a KO gene at the system-level. It enables ROC curve-based statistics analysis for assessing the performance of methods in terms of AUC (area under ROC curve), partial AUCs, Youden's best p-value threshold, specificity, sensitivity, accuracy, precision and recall. It is flexible to incorporate custom methods and currently integrates the state-of-the-art SPIA, ROntoTools (PE and pDIS), PADOG, GSA, GESA and SAFE. A benchmark dataset of mouse 10 KO GEO datasets is embedded for demo. The PathwayKO package provides a novel solution to the knock-out pathway enrichment analysis.

install.packages("remotes")
remotes::install_github("allenaigit/pathwayko")