How To Install r-bioc-dexseq on Debian 11
Introduction
In this tutorial we learn how to install r-bioc-dexseq on Debian 11.
What is r-bioc-dexseq
r-bioc-dexseq is:
The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.
There are three methods to install r-bioc-dexseq 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-dexseq 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-dexseq using apt-get by running the following command:
sudo apt-get -y install r-bioc-dexseq
Install r-bioc-dexseq Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-bioc-dexseq using apt by running the following command:
sudo apt -y install r-bioc-dexseq
Install r-bioc-dexseq 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-dexseq using aptitude by running the following command:
sudo aptitude -y install r-bioc-dexseq
How To Uninstall r-bioc-dexseq on Debian 11
To uninstall only the r-bioc-dexseq package we can use the following command:
sudo apt-get remove r-bioc-dexseq
Uninstall r-bioc-dexseq And Its Dependencies
To uninstall r-bioc-dexseq and its dependencies that are no longer needed by Debian 11, we can use the command below:
sudo apt-get -y autoremove r-bioc-dexseq
Remove r-bioc-dexseq Configurations and Data
To remove r-bioc-dexseq configuration and data from Debian 11 we can use the following command:
sudo apt-get -y purge r-bioc-dexseq
Remove r-bioc-dexseq configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-dexseq configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-dexseq
Dependencies
r-bioc-dexseq have the following dependencies:
- r-base-core
- r-api-4.0
- r-api-bioc-3.12
- r-bioc-biocparallel
- r-bioc-biobase
- r-bioc-summarizedexperiment
- r-bioc-iranges
- r-bioc-genomicranges
- r-bioc-deseq2
- r-bioc-annotationdbi
- r-cran-rcolorbrewer
- r-bioc-s4vectors
- r-bioc-biocgenerics
- r-bioc-biomart
- r-cran-hwriter
- r-cran-stringr
- r-bioc-rsamtools
- r-cran-statmod
- r-bioc-geneplotter
- r-bioc-genefilter
References
Summary
In this tutorial we learn how to install r-bioc-dexseq package on Debian 11 using different package management tools: apt, apt-get and aptitude.