How To Install r-bioc-biomart on Debian 12
Introduction
In this tutorial we learn how to install r-bioc-biomart on Debian 12.
What is r-bioc-biomart
r-bioc-biomart is:
In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.
There are three methods to install r-bioc-biomart 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-biomart 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-biomart using apt-get by running the following command:
sudo apt-get -y install r-bioc-biomart
Install r-bioc-biomart Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-bioc-biomart using apt by running the following command:
sudo apt -y install r-bioc-biomart
Install r-bioc-biomart 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-biomart using aptitude by running the following command:
sudo aptitude -y install r-bioc-biomart
How To Uninstall r-bioc-biomart on Debian 12
To uninstall only the r-bioc-biomart package we can use the following command:
sudo apt-get remove r-bioc-biomart
Uninstall r-bioc-biomart And Its Dependencies
To uninstall r-bioc-biomart and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove r-bioc-biomart
Remove r-bioc-biomart Configurations and Data
To remove r-bioc-biomart configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge r-bioc-biomart
Remove r-bioc-biomart configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-biomart configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-biomart
Dependencies
r-bioc-biomart have the following dependencies:
- r-base-core
- r-api-4.0
- r-api-bioc-3.16
- r-cran-xml
- r-bioc-annotationdbi
- r-cran-progress
- r-cran-stringr
- r-cran-httr
- r-cran-digest
- r-bioc-biocfilecache
- r-cran-rappdirs
- r-cran-xml2
References
Summary
In this tutorial we learn how to install r-bioc-biomart package on Debian 12 using different package management tools: apt, apt-get and aptitude.
