How To Install r-cran-alakazam on Kali Linux
Introduction
In this tutorial we learn how to install r-cran-alakazam
on Kali Linux.
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 Kali Linux. 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.
After updating apt database, We can install r-cran-alakazam
using apt-get
by running the following command:
Install r-cran-alakazam Using apt
Update apt database with apt
using the following command.
After updating apt database, We can install r-cran-alakazam
using apt
by running the following command:
Install r-cran-alakazam Using aptitude
If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude
using the following command.
After updating apt database, We can install r-cran-alakazam
using aptitude
by running the following command:
How To Uninstall r-cran-alakazam on Kali Linux
To uninstall only the r-cran-alakazam
package we can use the following command:
Uninstall r-cran-alakazam And Its Dependencies
To uninstall r-cran-alakazam
and its dependencies that are no longer needed by Kali Linux, we can use the command below:
Remove r-cran-alakazam Configurations and Data
To remove r-cran-alakazam
configuration and data from Kali Linux we can use the following command:
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:
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-bioc-biostrings
- r-cran-dplyr
- r-bioc-genomicalignments
- r-cran-igraph
- r-bioc-iranges
- r-cran-lazyeval
- 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
- libc6
- libgcc-s1
- libstdc++6
References
Summary
In this tutorial we learn how to install r-cran-alakazam
package on Kali Linux using different package management tools: apt
, apt-get
and aptitude
.