How To Install r-cran-tigger on Ubuntu

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

3 minutes • 599 words

Introduction

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

What is `r-cran-tigger`

r-cran-tigger is:

Summary: Infers the V genotype of an individual from immunoglobulin (Ig) repertoire-sequencing (Rep-Seq) data, including detection of any novel alleles. This information is then used to correct existing V allele calls from among the sample sequences.

High-throughput sequencing of B cell immunoglobulin receptors is providing unprecedented insight into adaptive immunity. A key step in analyzing these data involves assignment of the germline V, D and J gene segment alleles that comprise each immunoglobulin sequence by matching them against a database of known V(D)J alleles. However, this process will fail for sequences that utilize previously undetected alleles, whose frequency in the population is unclear.

TIgGER is a computational method that significantly improves V(D)J allele assignments by first determining the complete set of gene segments carried by an individual (including novel alleles) from V(D)J-rearrange sequences. TIgGER can then infer a subject’s genotype from these sequences, and use this genotype to correct the initial V(D)J allele assignments.

The application of TIgGER continues to identify a surprisingly high frequency of novel alleles in humans, highlighting the critical need for this approach. TIgGER, however, can and has been used with data from other species.

Core Abilities:

Detecting novel alleles
Inferring a subject’s genotype
Correcting preliminary allele calls

Required Input

A table of sequences from a single individual, with columns containing the following:
- V(D)J-rearranged nucleotide sequence (in IMGT-gapped format)
- Preliminary V allele calls
- Preliminary J allele calls
- Length of the junction region
Germline Ig sequences in IMGT-gapped fasta format (e.g., as those downloaded from IMGT/GENE-DB)

The former can be created through the use of IMGT/HighV-QUEST and Change-O.

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

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

Install r-cran-tigger Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install r-cran-tigger

Install r-cran-tigger 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-tigger using aptitude by running the following command:

sudo aptitude -y install r-cran-tigger

How To Uninstall r-cran-tigger on Ubuntu

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

sudo apt-get remove r-cran-tigger

Uninstall r-cran-tigger And Its Dependencies

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

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

Remove r-cran-tigger Configurations and Data

To remove r-cran-tigger configuration and data from Ubuntu we can use the following command:

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

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

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

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

Dependencies

r-cran-tigger have the following dependencies:

References

r-cran-tigger website

Summary

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