How To Install r-cran-shazam on Debian 10

Learn how to install r-cran-shazam on Debian 10 with this tutorial. r-cran-shazam is Immunoglobulin Somatic Hypermutation Analysis

Introduction

In this tutorial we learn how to install r-cran-shazam on Debian 10.

What is r-cran-shazam

r-cran-shazam is:

Provides a computational framework for Bayesian estimation of antigen-driven selection in immunoglobulin (Ig) sequences, providing an intuitive means of analyzing selection by quantifying the degree of selective pressure. Also provides tools to profile mutations in Ig sequences, build models of somatic hypermutation (SHM) in Ig sequences, and make model-dependent distance comparisons of Ig repertoires.

SHazaM is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) and provides tools for advanced analysis of somatic hypermutation (SHM) in immunoglobulin (Ig) sequences. Shazam focuses on the following analysis topics:

  • Quantification of mutational load SHazaM includes methods for determine the rate of observed and expected mutations under various criteria. Mutational profiling criteria include rates under SHM targeting models, mutations specific to CDR and FWR regions, and physicochemical property dependent substitution rates.
  • Statistical models of SHM targeting patterns Models of SHM may be divided into two independent components:
    1. a mutability model that defines where mutations occur and
    2. a nucleotide substitution model that defines the resulting mutation. Collectively these two components define an SHM targeting model. SHazaM provides empirically derived SHM 5-mer context mutation models for both humans and mice, as well tools to build SHM targeting models from data.
  • Analysis of selection pressure using BASELINe The Bayesian Estimation of Antigen-driven Selection in Ig Sequences (BASELINe) method is a novel method for quantifying antigen-driven selection in high-throughput Ig sequence data. BASELINe uses SHM targeting models can be used to estimate the null distribution of expected mutation frequencies, and provide measures of selection pressure informed by known AID targeting biases.
  • Model-dependent distance calculations SHazaM provides methods to compute evolutionary distances between sequences or set of sequences based on SHM targeting models. This information is particularly useful in understanding and defining clonal relationships.

There are three methods to install r-cran-shazam on Debian 10. 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-shazam 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-shazam using apt-get by running the following command:

sudo apt-get -y install r-cran-shazam

Install r-cran-shazam Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install r-cran-shazam

Install r-cran-shazam 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 Debian. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install r-cran-shazam using aptitude by running the following command:

sudo aptitude -y install r-cran-shazam

How To Uninstall r-cran-shazam on Debian 10

To uninstall only the r-cran-shazam package we can use the following command:

sudo apt-get remove r-cran-shazam

Uninstall r-cran-shazam And Its Dependencies

To uninstall r-cran-shazam and its dependencies that are no longer needed by Debian 10, we can use the command below:

sudo apt-get -y autoremove r-cran-shazam

Remove r-cran-shazam Configurations and Data

To remove r-cran-shazam configuration and data from Debian 10 we can use the following command:

sudo apt-get -y purge r-cran-shazam

Remove r-cran-shazam configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge r-cran-shazam

Dependencies

r-cran-shazam have the following dependencies:

References

Summary

In this tutorial we learn how to install r-cran-shazam package on Debian 10 using different package management tools: apt, apt-get and aptitude.