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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 with the execution of
the following command:
# commands for installing the package from github
devtools::install_github("Aitorzan3/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.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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