To install PathwaySpace, R version 4.4 or greater is required.
# Release version from CRAN
install.packages("PathwaySpace")# Dependencies to build the vignettes
install.packages("knitr")
install.packages("rmarkdown")
install.packages("remotes")
# Main packages
remotes::install_github("sysbiolab/RGraphSpace", build_vignettes=TRUE)
remotes::install_github("sysbiolab/PathwaySpace", build_vignettes=TRUE)
# Extension for spatial transcriptomics
remotes::install_github("sysbiolab/SpotSpace", build_vignettes=TRUE)
# Dependencies used in the extension
remotes::install_github("satijalab/Seurat")
remotes::install_github("satijalab/seurat-data")If you use PathwaySpace, please cite:
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
The PathwaySpace package is distributed under Artistic-2.0