How To Install r-bioc-progeny on Debian 12
Introduction
In this tutorial we learn how to install r-bioc-progeny on Debian 12.
What is r-bioc-progeny
r-bioc-progeny is:
This package provides a function to infer pathway activity from gene expression using PROGENy. It contains the linear model which is described in the publication “Perturbation-response genes reveal signaling footprints in cancer gene expression”.
There are three methods to install r-bioc-progeny on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install r-bioc-progeny Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install r-bioc-progeny using apt-get by running the following command:
sudo apt-get -y install r-bioc-progeny
Install r-bioc-progeny Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-bioc-progeny using apt by running the following command:
sudo apt -y install r-bioc-progeny
Install r-bioc-progeny Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install r-bioc-progeny using aptitude by running the following command:
sudo aptitude -y install r-bioc-progeny
How To Uninstall r-bioc-progeny on Debian 12
To uninstall only the r-bioc-progeny package we can use the following command:
sudo apt-get remove r-bioc-progeny
Uninstall r-bioc-progeny And Its Dependencies
To uninstall r-bioc-progeny and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove r-bioc-progeny
Remove r-bioc-progeny Configurations and Data
To remove r-bioc-progeny configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge r-bioc-progeny
Remove r-bioc-progeny configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-progeny configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-progeny
Dependencies
r-bioc-progeny have the following dependencies:
- r-base-core
- r-api-4.0
- r-api-bioc-3.16
- r-bioc-biobase
- r-cran-dplyr
- r-cran-tidyr
- r-cran-ggplot2
- r-cran-ggrepel
- r-cran-gridextra
- r-bioc-decoupler
- r-cran-reshape2
References
Summary
In this tutorial we learn how to install r-bioc-progeny package on Debian 12 using different package management tools: apt, apt-get and aptitude.
