pathwayPCA (https://www.bioconductor.org/packages/release/bioc/html/pathwayPCA.html) is an integrative pathway analysis software that utilizes modern statistical methodology on principal component analysis (PCA) and gene selection.
Odom GJ, Ban Y, Colaprico A, Liu L, Silva TC, Sun X, Pico AR, Zhang B, Wang L*, Chen X* (2020) pathwayPCA: an R package for integrative pathway analysis with modern PCA methodology and gene selection. Proteomics. 20(21-22):e1900409