To simplify the testing of CMS we have developed a R shiny app using our published classifier. The application can be found here as optimized for Nanostring platform.
The reference:
The underlying code is available here within the MD Anderson intranet.
For pre-clinical applications, we would recommend the following CMS caller which is not impacted by presence of nonhuman stroma, or absence of stroma.
CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models