How To Install r-bioc-purecn on Debian 11
Introduction
In this tutorial we learn how to install r-bioc-purecn on Debian 11.
What is r-bioc-purecn
r-bioc-purecn is:
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.
There are three methods to install r-bioc-purecn on Debian 11. 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-bioc-purecn 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-bioc-purecn using apt-get by running the following command:
sudo apt-get -y install r-bioc-purecn
Install r-bioc-purecn Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-bioc-purecn using apt by running the following command:
sudo apt -y install r-bioc-purecn
Install r-bioc-purecn 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-bioc-purecn using aptitude by running the following command:
sudo aptitude -y install r-bioc-purecn
How To Uninstall r-bioc-purecn on Debian 11
To uninstall only the r-bioc-purecn package we can use the following command:
sudo apt-get remove r-bioc-purecn
Uninstall r-bioc-purecn And Its Dependencies
To uninstall r-bioc-purecn and its dependencies that are no longer needed by Debian 11, we can use the command below:
sudo apt-get -y autoremove r-bioc-purecn
Remove r-bioc-purecn Configurations and Data
To remove r-bioc-purecn configuration and data from Debian 11 we can use the following command:
sudo apt-get -y purge r-bioc-purecn
Remove r-bioc-purecn configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-purecn configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-purecn
Dependencies
r-bioc-purecn have the following dependencies:
- r-base-core
- r-api-4.0
- r-api-bioc-3.12
- r-bioc-dnacopy
- r-bioc-variantannotation
- r-bioc-genomicranges
- r-bioc-iranges
- r-cran-rcolorbrewer
- r-bioc-s4vectors
- r-cran-data.table
- r-bioc-summarizedexperiment
- r-bioc-genomeinfodb
- r-bioc-genomicfeatures
- r-bioc-rsamtools
- r-bioc-biostrings
- r-bioc-biocgenerics
- r-bioc-rtracklayer
- r-cran-ggplot2
- r-cran-gridextra
- r-cran-futile.logger
- r-cran-vgam
- r-bioc-rhdf5
- r-cran-matrix
References
Summary
In this tutorial we learn how to install r-bioc-purecn package on Debian 11 using different package management tools: apt, apt-get and aptitude.