How To Install r-bioc-gviz on Debian 9

In this tutorial we learn how to install r-bioc-gviz on Debian 9. r-bioc-gviz is Plotting data and annotation information along genomic coordinates

Introduction

In this tutorial we learn how to install r-bioc-gviz on Debian 9.

What is r-bioc-gviz

r-bioc-gviz is:

Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.

There are three methods to install r-bioc-gviz on Debian 9. 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-gviz 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-gviz using apt-get by running the following command:

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

Install r-bioc-gviz Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install r-bioc-gviz

Install r-bioc-gviz 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-gviz using aptitude by running the following command:

sudo aptitude -y install r-bioc-gviz

How To Uninstall r-bioc-gviz on Debian 9

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

sudo apt-get remove r-bioc-gviz

Uninstall r-bioc-gviz And Its Dependencies

To uninstall r-bioc-gviz and its dependencies that are no longer needed by Debian 9, we can use the command below:

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

Remove r-bioc-gviz Configurations and Data

To remove r-bioc-gviz configuration and data from Debian 9 we can use the following command:

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

Remove r-bioc-gviz configuration, data, and all of its dependencies

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

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

Dependencies

r-bioc-gviz have the following dependencies:

References

Summary

In this tutorial we learn how to install r-bioc-gviz package on Debian 9 using different package management tools: apt, apt-get and aptitude.