How To Install r-bioc-tcgabiolinks on Debian 11

In this tutorial we learn how to install r-bioc-tcgabiolinks on Debian 11. r-bioc-tcgabiolinks is GNU R/Bioconductor package for integrative analysis with GDC data

Introduction

In this tutorial we learn how to install r-bioc-tcgabiolinks on Debian 11.

r-bioc-tcgabiolinks is:

The aim of TCGAbiolinks is:

  1. facilitate the GDC open-access data retrieval,
  2. prepare the data using the appropriate pre-processing strategies,
  3. provide the means to carry out different standard analyses and
  4. to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.

There are three methods to install r-bioc-tcgabiolinks on Debian 11. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install r-bioc-tcgabiolinks using apt-get by running the following command:

sudo apt-get -y install r-bioc-tcgabiolinks

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install r-bioc-tcgabiolinks using apt by running the following command:

sudo apt -y install r-bioc-tcgabiolinks

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-tcgabiolinks using aptitude by running the following command:

sudo aptitude -y install r-bioc-tcgabiolinks

To uninstall only the r-bioc-tcgabiolinks package we can use the following command:

sudo apt-get remove r-bioc-tcgabiolinks

To uninstall r-bioc-tcgabiolinks and its dependencies that are no longer needed by Debian 11, we can use the command below:

sudo apt-get -y autoremove r-bioc-tcgabiolinks

To remove r-bioc-tcgabiolinks configuration and data from Debian 11 we can use the following command:

sudo apt-get -y purge r-bioc-tcgabiolinks

We can use the following command to remove r-bioc-tcgabiolinks configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge r-bioc-tcgabiolinks

Dependencies

r-bioc-tcgabiolinks have the following dependencies:

References

Summary

In this tutorial we learn how to install r-bioc-tcgabiolinks package on Debian 11 using different package management tools: apt, apt-get and aptitude.