How To Install r-bioc-scran on Debian 12
Introduction
In this tutorial we learn how to install r-bioc-scran on Debian 12.
What is r-bioc-scran
r-bioc-scran is:
Implements functions for low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, detection of highly variable and significantly correlated genes, identification of marker genes, and other common tasks in routine single-cell analysis workflows.
There are three methods to install r-bioc-scran 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-scran 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-scran using apt-get by running the following command:
sudo apt-get -y install r-bioc-scran
Install r-bioc-scran Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-bioc-scran using apt by running the following command:
sudo apt -y install r-bioc-scran
Install r-bioc-scran 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-scran using aptitude by running the following command:
sudo aptitude -y install r-bioc-scran
How To Uninstall r-bioc-scran on Debian 12
To uninstall only the r-bioc-scran package we can use the following command:
sudo apt-get remove r-bioc-scran
Uninstall r-bioc-scran And Its Dependencies
To uninstall r-bioc-scran and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove r-bioc-scran
Remove r-bioc-scran Configurations and Data
To remove r-bioc-scran configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge r-bioc-scran
Remove r-bioc-scran configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-scran configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-scran
Dependencies
r-bioc-scran have the following dependencies:
- r-base-core
- r-api-4.0
- r-api-bioc-3.16
- r-bioc-singlecellexperiment
- r-bioc-scuttle
- r-bioc-summarizedexperiment
- r-bioc-s4vectors
- r-bioc-biocgenerics
- r-bioc-biocparallel
- r-cran-rcpp
- r-cran-matrix
- r-bioc-edger
- r-bioc-limma
- r-cran-igraph
- r-cran-statmod
- r-bioc-delayedarray
- r-bioc-delayedmatrixstats
- r-bioc-biocsingular
- r-bioc-bluster
- r-bioc-metapod
- r-cran-dqrng
- r-bioc-beachmat
- r-cran-bh
- libc6
- libgcc-s1
- liblapack3
- libstdc++6
References
Summary
In this tutorial we learn how to install r-bioc-scran package on Debian 12 using different package management tools: apt, apt-get and aptitude.
