How To Install r-bioc-purecn on Kali Linux

In this tutorial we learn how to install r-bioc-purecn on Kali Linux. r-bioc-purecn is copy number calling and SNV classification using targeted short read sequencing

Introduction

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

What is r-bioc-purecn

r-bioc-purecn is:

This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.

There are three methods to install r-bioc-purecn 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-purecn 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-purecn using apt-get by running the following command:

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

Install r-bioc-purecn Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install r-bioc-purecn

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

sudo aptitude -y install r-bioc-purecn

How To Uninstall r-bioc-purecn on Kali Linux

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

sudo apt-get remove r-bioc-purecn

Uninstall r-bioc-purecn And Its Dependencies

To uninstall r-bioc-purecn and its dependencies that are no longer needed by Kali Linux, we can use the command below:

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

Remove r-bioc-purecn Configurations and Data

To remove r-bioc-purecn configuration and data from Kali Linux we can use the following command:

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

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

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

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

Dependencies

r-bioc-purecn have the following dependencies:

References

Summary

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