How To Install r-bioc-biomart on Kali Linux

In this tutorial we learn how to install r-bioc-biomart on Kali Linux. r-bioc-biomart is GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)

Introduction

In this tutorial we learn how to install r-bioc-biomart on Kali Linux.

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 Kali Linux. 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 on Kali Linux first since aptitude is usually not installed by default on Kali Linux. 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 Kali Linux

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 Kali Linux, 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 Kali Linux 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:

References

Summary

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