To install PathwaySpace, R version 4.5 or greater is required.
Release version
# Release version from CRAN
install.packages("PathwaySpace")Development version
# Dependencies to build the vignettes
install.packages("knitr")
install.packages("rmarkdown")
install.packages("remotes")
# Package source
remotes::install_github("sysbiolab/RGraphSpace", build_vignettes=TRUE)
remotes::install_github("sysbiolab/PathwaySpace", build_vignettes=TRUE)Other packages used in the tutorials
install.packages("Seurat")
install.packages("hdf5r")
install.packages("arrow")
install.packages("lfl")
remotes::install_github("satijalab/Seurat")
remotes::install_github("satijalab/seurat-data")
install.packages("BiocManager")
BiocManager::install("glmGamPoi")Citation
Tercan & Apolonio et al. Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods. STAR Protocols, 2025. https://doi.org/10.1016/j.xpro.2025.103681
Ellrott et al. Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets. Cancer Cell, 2025. https://doi.org/10.1016/j.ccell.2024.12.002
Licenses
The PathwaySpace package is distributed under Artistic-2.0