How To Install r-bioc-ensembldb on Debian 12
Introduction
In this tutorial we learn how to install r-bioc-ensembldb on Debian 12.
What is r-bioc-ensembldb
r-bioc-ensembldb is:
The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the ensembldb package provides also a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes.
There are three methods to install r-bioc-ensembldb 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-ensembldb 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-ensembldb using apt-get by running the following command:
sudo apt-get -y install r-bioc-ensembldb
Install r-bioc-ensembldb Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-bioc-ensembldb using apt by running the following command:
sudo apt -y install r-bioc-ensembldb
Install r-bioc-ensembldb 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-ensembldb using aptitude by running the following command:
sudo aptitude -y install r-bioc-ensembldb
How To Uninstall r-bioc-ensembldb on Debian 12
To uninstall only the r-bioc-ensembldb package we can use the following command:
sudo apt-get remove r-bioc-ensembldb
Uninstall r-bioc-ensembldb And Its Dependencies
To uninstall r-bioc-ensembldb and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove r-bioc-ensembldb
Remove r-bioc-ensembldb Configurations and Data
To remove r-bioc-ensembldb configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge r-bioc-ensembldb
Remove r-bioc-ensembldb configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-ensembldb configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-ensembldb
Dependencies
r-bioc-ensembldb have the following dependencies:
- r-base-core
- r-api-4.0
- r-api-bioc-3.16
- r-bioc-biocgenerics
- r-bioc-genomicranges
- r-bioc-genomicfeatures
- r-bioc-annotationfilter
- r-cran-rsqlite
- r-cran-dbi
- r-bioc-biobase
- r-bioc-genomeinfodb
- r-bioc-annotationdbi
- r-bioc-rtracklayer
- r-bioc-s4vectors
- r-bioc-rsamtools
- r-bioc-iranges
- r-bioc-protgenerics
- r-bioc-biostrings
- r-cran-curl
References
Summary
In this tutorial we learn how to install r-bioc-ensembldb package on Debian 12 using different package management tools: apt, apt-get and aptitude.