How To Install r-bioc-gviz on Debian 10
Introduction
In this tutorial we learn how to install r-bioc-gviz on Debian 10.
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 10. 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 10
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 10, 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 10 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:
- r-base-core
- r-api-3.5
- r-api-bioc-3.8
- r-bioc-s4vectors
- r-bioc-iranges
- r-bioc-genomicranges
- r-bioc-xvector
- r-bioc-rtracklayer
- r-cran-lattice
- r-cran-rcolorbrewer
- r-bioc-biomart
- r-bioc-annotationdbi
- r-bioc-biobase
- r-bioc-genomicfeatures
- r-bioc-bsgenome
- r-bioc-biostrings
- r-bioc-biovizbase
- r-bioc-rsamtools
- r-cran-latticeextra
- r-cran-matrixstats
- r-bioc-genomicalignments
- r-bioc-genomeinfodb
- r-bioc-biocgenerics
- r-cran-digest
References
Summary
In this tutorial we learn how to install r-bioc-gviz package on Debian 10 using different package management tools: apt, apt-get and aptitude.