How To Install r-cran-alakazam on Ubuntu

Posted on April 1, 2023 (Last modified on May 20, 2023 )

3 minutes • 476 words

Introduction

In this tutorial we learn how to install r-cran-alakazam on Ubuntu.

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. 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

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, 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 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

Dependencies

r-cran-alakazam have the following dependencies:

References

r-cran-alakazam website

Summary

In this tutorial we learn how to install r-cran-alakazam package on Ubuntu using different package management tools: apt, apt-get and aptitude.