How To Install r-bioc-megadepth on Debian 12
Introduction
In this tutorial we learn how to install r-bioc-megadepth on Debian 12.
What is r-bioc-megadepth
r-bioc-megadepth is:
This package provides an R interface to Megadepth by Christopher Wilks available at https://github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files. Megadepth was used to create the raw files provided by https://bioconductor.org/packages/recount3.
There are three methods to install r-bioc-megadepth 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-megadepth 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-megadepth using apt-get by running the following command:
sudo apt-get -y install r-bioc-megadepth
Install r-bioc-megadepth Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-bioc-megadepth using apt by running the following command:
sudo apt -y install r-bioc-megadepth
Install r-bioc-megadepth 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-megadepth using aptitude by running the following command:
sudo aptitude -y install r-bioc-megadepth
How To Uninstall r-bioc-megadepth on Debian 12
To uninstall only the r-bioc-megadepth package we can use the following command:
sudo apt-get remove r-bioc-megadepth
Uninstall r-bioc-megadepth And Its Dependencies
To uninstall r-bioc-megadepth and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove r-bioc-megadepth
Remove r-bioc-megadepth Configurations and Data
To remove r-bioc-megadepth configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge r-bioc-megadepth
Remove r-bioc-megadepth configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-megadepth configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-megadepth
Dependencies
r-bioc-megadepth have the following dependencies:
- r-base-core
- r-api-4.0
- r-api-bioc-3.16
- r-cran-xfun
- r-cran-fs
- r-bioc-genomicranges
- r-cran-readr
- r-cran-cmdfun
- r-cran-dplyr
- r-cran-magrittr
- megadepth
References
Summary
In this tutorial we learn how to install r-bioc-megadepth package on Debian 12 using different package management tools: apt, apt-get and aptitude.
