How To Install r-bioc-fishpond on Debian 12
Introduction
In this tutorial we learn how to install r-bioc-fishpond on Debian 12.
What is r-bioc-fishpond
r-bioc-fishpond is:
Fishpond contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling. Also the package contains utilities for working with Salmon and Alevin quantification files.
There are three methods to install r-bioc-fishpond 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-fishpond 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-fishpond using apt-get by running the following command:
sudo apt-get -y install r-bioc-fishpond
Install r-bioc-fishpond Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-bioc-fishpond using apt by running the following command:
sudo apt -y install r-bioc-fishpond
Install r-bioc-fishpond 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-fishpond using aptitude by running the following command:
sudo aptitude -y install r-bioc-fishpond
How To Uninstall r-bioc-fishpond on Debian 12
To uninstall only the r-bioc-fishpond package we can use the following command:
sudo apt-get remove r-bioc-fishpond
Uninstall r-bioc-fishpond And Its Dependencies
To uninstall r-bioc-fishpond and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove r-bioc-fishpond
Remove r-bioc-fishpond Configurations and Data
To remove r-bioc-fishpond configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge r-bioc-fishpond
Remove r-bioc-fishpond configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-fishpond configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-fishpond
Dependencies
r-bioc-fishpond have the following dependencies:
- r-base-core
- r-api-4.0
- r-api-bioc-3.16
- r-cran-abind
- r-cran-gtools
- r-bioc-qvalue
- r-bioc-s4vectors
- r-bioc-iranges
- r-bioc-summarizedexperiment
- r-bioc-genomicranges
- r-cran-matrixstats
- r-cran-svmisc
- r-cran-matrix
- r-bioc-singlecellexperiment
- r-cran-jsonlite
References
Summary
In this tutorial we learn how to install r-bioc-fishpond package on Debian 12 using different package management tools: apt, apt-get and aptitude.