README.md
In GeRnika: Simulation, Visualization and Comparison of Tumor Evolution Data

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GeRnika is an open-source R package that is capable of simulating, visualizing and comparing tumor evolution data by using simple commands. This aims at providing a tool to help researchers to easily simulate tumor clonal data and analyze the results of their approaches for studying the composition and the evolutionary history of tumors.

GeRnika may be easily installed from CRAN with the execution of the following command:

# commands for installing the package from github
install.packages("GeRnika")

Note that in order to install the vignettes together with the package, it is necessary to attach the packages “rmarkdown”, “knitcitations”, “knitr” and “ggpubr” to your namespace. If you have not installed them yet, you can do it by using the following command:

# commands for installing the package together with its vignettes from github
install.packages(c("rmarkdown", "knitcitations", "knitr", "ggpubr"))

Once you have done that, you may use the following instruction to install de vignettes of GeRnika:

# commands for installing the package together with its vignettes from github
devtools::install_github("Aitorzan3/GeRnika", build_vignettes = TRUE)

Once the package has been installed, the namespace of GeRnika may be loaded by using

library(GeRnika)

This produces a short report about the versions of the packages that are used by GeRnika, providing information about any conflict related to its dependencies.

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GeRnika")

Regarding the principles related to the design of GeRnika, this has been implemented in order to be fundamentally intuitive and easy to use. This is achieved by offering accesible methods for simulating and analyzing tumor phylogenies by using simple commands, all in one single package.