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Install

2026-09-01

Install.rmd

How to Install

Using pak

OncoProflingTools (OPT) is currently available from our GitHub repository while in active development. In the future, we plan to make it available on CRAN or Bioconductor.

Ensure R version 4.0 or greater is installed. To install OPT, run the following command in the R console:

install.packages("pak") # alternatively, use native R package manager
pak::pkg_install("TYCGenomicsLab/OncoProfilingTools") # will fetch from GitHub
library(OncoProfilingTools)

Dependencies

It is highly recommended you also install and load dplyr, MultiAssayExperiment, and SummarizedExperiment to make use of the full functionality of OPT. To install these packages, run:

# pak will automatically know to use CRAN or Bioconductor
pak::pkg_install(c("dplyr", "MultiAssayExperiment", "SummarizedExperiment"))
library("dplyr")
library("MultiAssayExperiment")
library("SummarizedExperiment")

Pak will automatically install any dependencies required by OPT. If you recieve any issues about missing packages, please install them manually.