How To Install r-bioc-scater on Debian 12
Introduction
In this tutorial we learn how to install r-bioc-scater on Debian 12.
What is r-bioc-scater
r-bioc-scater is:
A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.
There are three methods to install r-bioc-scater 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-scater 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-scater using apt-get by running the following command:
sudo apt-get -y install r-bioc-scater
Install r-bioc-scater Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-bioc-scater using apt by running the following command:
sudo apt -y install r-bioc-scater
Install r-bioc-scater 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-scater using aptitude by running the following command:
sudo aptitude -y install r-bioc-scater
How To Uninstall r-bioc-scater on Debian 12
To uninstall only the r-bioc-scater package we can use the following command:
sudo apt-get remove r-bioc-scater
Uninstall r-bioc-scater And Its Dependencies
To uninstall r-bioc-scater and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove r-bioc-scater
Remove r-bioc-scater Configurations and Data
To remove r-bioc-scater configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge r-bioc-scater
Remove r-bioc-scater configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-scater configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-scater
Dependencies
r-bioc-scater have the following dependencies:
- r-base-core
- r-api-4.0
- r-api-bioc-3.16
- r-bioc-singlecellexperiment
- r-bioc-scuttle
- r-cran-ggplot2
- r-cran-gridextra
- r-cran-matrix
- r-bioc-biocgenerics
- r-bioc-s4vectors
- r-bioc-summarizedexperiment
- r-bioc-delayedarray
- r-bioc-delayedmatrixstats
- r-bioc-beachmat
- r-bioc-biocneighbors
- r-bioc-biocsingular
- r-bioc-biocparallel
- r-cran-rlang
- r-cran-ggbeeswarm
- r-cran-viridis
- r-cran-rtsne
- r-cran-rcolorbrewer
- r-cran-rcppml
- r-cran-uwot
- r-cran-pheatmap
- r-cran-ggrastr
- r-cran-ggrepel
References
Summary
In this tutorial we learn how to install r-bioc-scater package on Debian 12 using different package management tools: apt, apt-get and aptitude.
