How To Install r-bioc-edaseq on Debian 12
Introduction
In this tutorial we learn how to install r-bioc-edaseq on Debian 12.
What is r-bioc-edaseq
r-bioc-edaseq is:
Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).
There are three methods to install r-bioc-edaseq 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-edaseq 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-edaseq using apt-get by running the following command:
sudo apt-get -y install r-bioc-edaseq
Install r-bioc-edaseq Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-bioc-edaseq using apt by running the following command:
sudo apt -y install r-bioc-edaseq
Install r-bioc-edaseq 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-edaseq using aptitude by running the following command:
sudo aptitude -y install r-bioc-edaseq
How To Uninstall r-bioc-edaseq on Debian 12
To uninstall only the r-bioc-edaseq package we can use the following command:
sudo apt-get remove r-bioc-edaseq
Uninstall r-bioc-edaseq And Its Dependencies
To uninstall r-bioc-edaseq and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove r-bioc-edaseq
Remove r-bioc-edaseq Configurations and Data
To remove r-bioc-edaseq configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge r-bioc-edaseq
Remove r-bioc-edaseq configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-edaseq configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-edaseq
Dependencies
r-bioc-edaseq have the following dependencies:
- r-base-core
- r-api-4.0
- r-api-bioc-3.16
- r-bioc-biobase
- r-bioc-shortread
- r-bioc-biocgenerics
- r-bioc-iranges
- r-bioc-aroma.light
- r-bioc-rsamtools
- r-bioc-biomart
- r-bioc-biostrings
- r-bioc-annotationdbi
- r-bioc-genomicfeatures
- r-bioc-genomicranges
- r-cran-biocmanager
References
Summary
In this tutorial we learn how to install r-bioc-edaseq package on Debian 12 using different package management tools: apt, apt-get and aptitude.
