How To Install r-cran-alakazam on Ubuntu 20.04
Introduction
In this tutorial we learn how to install r-cran-alakazam
on Ubuntu 20.04.
What is r-cran-alakazam
r-cran-alakazam is:
Alakazam is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) and provides a set of tools to investigate lymphocyte receptor clonal lineages, diversity, gene usage, and other repertoire level properties, with a focus on high-throughput immunoglobulin (Ig) sequencing.
Alakazam serves five main purposes:
- Providing core functionality for other R packages in the Immcantation framework. This includes common tasks such as file I/O, basic DNA sequence manipulation, and interacting with V(D)J segment and gene annotations.
- Providing an R interface for interacting with the output of the pRESTO and Change-O tool suites.
- Performing lineage reconstruction on clonal populations of Ig sequences and analyzing the topology of the resultant lineage trees.
- Performing clonal abundance and diversity analysis on lymphocyte repertoires.
- Performing physicochemical property analyses of lymphocyte receptor sequences.
There are three methods to install r-cran-alakazam
on Ubuntu 20.04. 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-cran-alakazam 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-cran-alakazam
using apt-get
by running the following command:
sudo apt-get -y install r-cran-alakazam
Install r-cran-alakazam Using apt
Update apt database with apt
using the following command.
sudo apt update
After updating apt database, We can install r-cran-alakazam
using apt
by running the following command:
sudo apt -y install r-cran-alakazam
Install r-cran-alakazam 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 Ubuntu. Update apt database with aptitude
using the following command.
sudo aptitude update
After updating apt database, We can install r-cran-alakazam
using aptitude
by running the following command:
sudo aptitude -y install r-cran-alakazam
How To Uninstall r-cran-alakazam on Ubuntu 20.04
To uninstall only the r-cran-alakazam
package we can use the following command:
sudo apt-get remove r-cran-alakazam
Uninstall r-cran-alakazam And Its Dependencies
To uninstall r-cran-alakazam
and its dependencies that are no longer needed by Ubuntu 20.04, we can use the command below:
sudo apt-get -y autoremove r-cran-alakazam
Remove r-cran-alakazam Configurations and Data
To remove r-cran-alakazam
configuration and data from Ubuntu 20.04 we can use the following command:
sudo apt-get -y purge r-cran-alakazam
Remove r-cran-alakazam configuration, data, and all of its dependencies
We can use the following command to remove r-cran-alakazam
configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-cran-alakazam
References
Summary
In this tutorial we learn how to install r-cran-alakazam
package on Ubuntu 20.04 using different package management tools: apt
, apt-get
and aptitude
.