How To Install r-bioc-mofa on Debian 12
Introduction
In this tutorial we learn how to install r-bioc-mofa on Debian 12.
What is r-bioc-mofa
r-bioc-mofa is:
Multi-Omics Factor Analysis: an unsupervised framework for the integration of multi-omics data sets.
Upstream no longer supports this package. This package only still ships to help with rerunning/comparing/transitioning existing projects. For new projects please upgrade to MOFA2 (MOFA+). Actually, also when adding new data to old projects, MOFA2 has further improved the handling of multiple factors, and to compensate for a batch effect that is likely introduced with additional data, may be an immediate use case for that new version.
There are three methods to install r-bioc-mofa 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-mofa 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-mofa using apt-get by running the following command:
sudo apt-get -y install r-bioc-mofa
Install r-bioc-mofa Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-bioc-mofa using apt by running the following command:
sudo apt -y install r-bioc-mofa
Install r-bioc-mofa 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-mofa using aptitude by running the following command:
sudo aptitude -y install r-bioc-mofa
How To Uninstall r-bioc-mofa on Debian 12
To uninstall only the r-bioc-mofa package we can use the following command:
sudo apt-get remove r-bioc-mofa
Uninstall r-bioc-mofa And Its Dependencies
To uninstall r-bioc-mofa and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove r-bioc-mofa
Remove r-bioc-mofa Configurations and Data
To remove r-bioc-mofa configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge r-bioc-mofa
Remove r-bioc-mofa configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-mofa configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-mofa
Dependencies
r-bioc-mofa have the following dependencies:
- r-base-core
- r-api-4.0
- r-api-bioc-3.16
- r-bioc-rhdf5
- r-cran-dplyr
- r-cran-reshape2
- r-cran-pheatmap
- r-cran-corrplot
- r-cran-ggplot2
- r-cran-ggbeeswarm
- r-cran-scales
- r-cran-ggally
- r-cran-rcolorbrewer
- r-cran-cowplot
- r-cran-ggrepel
- r-bioc-multiassayexperiment
- r-bioc-biobase
- r-cran-doparallel
- r-cran-foreach
- r-cran-reticulate
- python3-mofapy
References
Summary
In this tutorial we learn how to install r-bioc-mofa package on Debian 12 using different package management tools: apt, apt-get and aptitude.
