How To Install r-cran-tigger on Ubuntu 22.04
Introduction
In this tutorial we learn how to install r-cran-tigger
on Ubuntu 22.04.
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 22.04. 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-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 22.04
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 22.04, 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 22.04 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
References
Summary
In this tutorial we learn how to install r-cran-tigger
package on Ubuntu 22.04 using different package management tools: apt
, apt-get
and aptitude
.