How To Install r-bioc-rgsepd on Debian 11
Introduction
In this tutorial we learn how to install r-bioc-rgsepd on Debian 11.
What is r-bioc-rgsepd
r-bioc-rgsepd is:
R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at transcript IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.
There are three methods to install r-bioc-rgsepd 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-rgsepd 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-rgsepd using apt-get by running the following command:
sudo apt-get -y install r-bioc-rgsepd
Install r-bioc-rgsepd Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-bioc-rgsepd using apt by running the following command:
sudo apt -y install r-bioc-rgsepd
Install r-bioc-rgsepd 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-rgsepd using aptitude by running the following command:
sudo aptitude -y install r-bioc-rgsepd
How To Uninstall r-bioc-rgsepd on Debian 11
To uninstall only the r-bioc-rgsepd package we can use the following command:
sudo apt-get remove r-bioc-rgsepd
Uninstall r-bioc-rgsepd And Its Dependencies
To uninstall r-bioc-rgsepd and its dependencies that are no longer needed by Debian 11, we can use the command below:
sudo apt-get -y autoremove r-bioc-rgsepd
Remove r-bioc-rgsepd Configurations and Data
To remove r-bioc-rgsepd configuration and data from Debian 11 we can use the following command:
sudo apt-get -y purge r-bioc-rgsepd
Remove r-bioc-rgsepd configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-rgsepd configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-rgsepd
Dependencies
r-bioc-rgsepd have the following dependencies:
- r-base-core
- r-api-4.0
- r-api-bioc-3.12
- r-bioc-deseq2
- r-bioc-goseq
- r-cran-gplots
- r-bioc-biomart
- r-bioc-org.hs.eg.db
- r-bioc-go.db
- r-bioc-summarizedexperiment
- r-cran-hash
- r-bioc-annotationdbi
References
Summary
In this tutorial we learn how to install r-bioc-rgsepd package on Debian 11 using different package management tools: apt, apt-get and aptitude.
