How To Install r-cran-alakazam on Debian 12
Introduction
In this tutorial we learn how to install r-cran-alakazam on Debian 12.
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 Debian 12. 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 Debian. 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 Debian 12
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 Debian 12, 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 Debian 12 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:
- r-base-core
- r-api-4.0
- r-cran-ggplot2
- r-cran-airr
- r-cran-ape
- r-cran-dplyr
- r-cran-igraph
- r-cran-matrix
- r-cran-progress
- r-cran-rcpp
- r-cran-readr
- r-cran-rlang
- r-cran-scales
- r-cran-seqinr
- r-cran-stringi
- r-cran-tibble
- r-cran-tidyr
- r-bioc-biostrings
- r-bioc-genomicalignments
- r-bioc-iranges
- libc6
- libgcc-s1
- libstdc++6
References
Summary
In this tutorial we learn how to install r-cran-alakazam package on Debian 12 using different package management tools: apt, apt-get and aptitude.
