How To Install r-cran-sctransform on Debian 12
Introduction
In this tutorial we learn how to install r-cran-sctransform on Debian 12.
What is r-cran-sctransform
r-cran-sctransform is:
A normalization method for single-cell UMI count data using a variance stabilizing transformation. The transformation is based on a negative binomial regression model with regularized parameters. As part of the same regression framework, this package also provides functions for batch correction, and data correction. See Hafemeister and Satija 2019 doi:10.1101/576827 for more details.
There are three methods to install r-cran-sctransform 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-cran-sctransform 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-cran-sctransform using apt-get by running the following command:
sudo apt-get -y install r-cran-sctransform
Install r-cran-sctransform Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-cran-sctransform using apt by running the following command:
sudo apt -y install r-cran-sctransform
Install r-cran-sctransform 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-cran-sctransform using aptitude by running the following command:
sudo aptitude -y install r-cran-sctransform
How To Uninstall r-cran-sctransform on Debian 12
To uninstall only the r-cran-sctransform package we can use the following command:
sudo apt-get remove r-cran-sctransform
Uninstall r-cran-sctransform And Its Dependencies
To uninstall r-cran-sctransform and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove r-cran-sctransform
Remove r-cran-sctransform Configurations and Data
To remove r-cran-sctransform configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge r-cran-sctransform
Remove r-cran-sctransform configuration, data, and all of its dependencies
We can use the following command to remove r-cran-sctransform configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-cran-sctransform
Dependencies
r-cran-sctransform have the following dependencies:
- r-base-core
- r-api-4.0
- r-cran-dplyr
- r-cran-magrittr
- r-cran-mass
- r-cran-matrix
- r-cran-future.apply
- r-cran-future
- r-cran-ggplot2
- r-cran-reshape2
- r-cran-rlang
- r-cran-gridextra
- r-cran-matrixstats
- r-cran-rcpparmadillo
- r-cran-rcpp
- libblas3
- libc6
- libgcc-s1
- liblapack3
- libstdc++6
References
Summary
In this tutorial we learn how to install r-cran-sctransform package on Debian 12 using different package management tools: apt, apt-get and aptitude.
