How To Install r-bioc-degreport on Debian 12
Introduction
In this tutorial we learn how to install r-bioc-degreport on Debian 12.
What is r-bioc-degreport
r-bioc-degreport is:
Creation of a HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.
There are three methods to install r-bioc-degreport 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-bioc-degreport 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-degreport using apt-get by running the following command:
sudo apt-get -y install r-bioc-degreport
Install r-bioc-degreport Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-bioc-degreport using apt by running the following command:
sudo apt -y install r-bioc-degreport
Install r-bioc-degreport 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-degreport using aptitude by running the following command:
sudo aptitude -y install r-bioc-degreport
How To Uninstall r-bioc-degreport on Debian 12
To uninstall only the r-bioc-degreport package we can use the following command:
sudo apt-get remove r-bioc-degreport
Uninstall r-bioc-degreport And Its Dependencies
To uninstall r-bioc-degreport and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove r-bioc-degreport
Remove r-bioc-degreport Configurations and Data
To remove r-bioc-degreport configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge r-bioc-degreport
Remove r-bioc-degreport configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-degreport configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-degreport
Dependencies
r-bioc-degreport have the following dependencies:
- r-base-core
- r-api-4.0
- r-api-bioc-3.16
- r-bioc-biobase
- r-bioc-biocgenerics
- r-cran-broom
- r-cran-circlize
- r-bioc-complexheatmap
- r-cran-cowplot
- r-bioc-consensusclusterplus
- r-cran-cluster
- r-bioc-deseq2
- r-cran-dplyr
- r-bioc-edger
- r-cran-ggplot2
- r-cran-ggdendro
- r-cran-ggrepel
- r-cran-knitr
- r-cran-logging
- r-cran-magrittr
- r-cran-psych
- r-cran-rcolorbrewer
- r-cran-reshape
- r-cran-rlang
- r-cran-scales
- r-cran-stringr
- r-bioc-s4vectors
- r-bioc-summarizedexperiment
- r-cran-tidyr
- r-cran-tibble
References
Summary
In this tutorial we learn how to install r-bioc-degreport package on Debian 12 using different package management tools: apt, apt-get and aptitude.
