How To Install r-bioc-bitseq on Kali Linux

In this tutorial we learn how to install r-bioc-bitseq on Kali Linux. r-bioc-bitseq is transcript expression inference and analysis for RNA-seq data

Introduction

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

What is r-bioc-bitseq

r-bioc-bitseq is:

The BitSeq package is targeted for transcript expression analysis and differential expression analysis of RNA-seq data in two stage process. In the first stage it uses Bayesian inference methodology to infer expression of individual transcripts from individual RNA-seq experiments. The second stage of BitSeq embraces the differential expression analysis of transcript expression. Providing expression estimates from replicates of multiple conditions, Log-Normal model of the estimates is used for inferring the condition mean transcript expression and ranking the transcripts based on the likelihood of differential expression.

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

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

Install r-bioc-bitseq Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install r-bioc-bitseq

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

sudo aptitude -y install r-bioc-bitseq

How To Uninstall r-bioc-bitseq on Kali Linux

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

sudo apt-get remove r-bioc-bitseq

Uninstall r-bioc-bitseq And Its Dependencies

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

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

Remove r-bioc-bitseq Configurations and Data

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

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

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

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

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

Dependencies

r-bioc-bitseq have the following dependencies:

References

Summary

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