How To Install r-bioc-bitseq on Kali Linux
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:
- r-base-core
- r-api-4.0
- r-api-bioc-3.12
- r-bioc-rsamtools
- r-bioc-s4vectors
- r-bioc-iranges
- r-bioc-rhtslib
- libc6
- libcurl4
- libgcc-s1
- libgomp1
- libstdc++6
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
.