How To Install r-bioc-sva on Debian 12

Learn how to install r-bioc-sva on Debian 12 with this tutorial. r-bioc-sva is GNU R Surrogate Variable Analysis

Introduction

In this tutorial we learn how to install r-bioc-sva on Debian 12.

What is `r-bioc-sva`

r-bioc-sva is:

The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data (like gene expression/RNA sequencing/methylation/brain imaging data) that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise. The sva package can be used to remove artifacts in three ways: (1) identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments (Leek and Storey 2007 PLoS Genetics,2008 PNAS), (2) directly removing known batch effects using ComBat (Johnson et al. 2007 Biostatistics) and (3) removing batch effects with known control probes (Leek 2014 biorXiv). Removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews Genetics).

There are three methods to install r-bioc-sva 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-sva 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-sva using apt-get by running the following command:

sudo apt-get -y install r-bioc-sva

Install r-bioc-sva Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install r-bioc-sva using apt by running the following command:

sudo apt -y install r-bioc-sva

Install r-bioc-sva 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-sva using aptitude by running the following command:

sudo aptitude -y install r-bioc-sva

How To Uninstall r-bioc-sva on Debian 12

To uninstall only the r-bioc-sva package we can use the following command:

sudo apt-get remove r-bioc-sva

Uninstall r-bioc-sva And Its Dependencies

To uninstall r-bioc-sva and its dependencies that are no longer needed by Debian 12, we can use the command below:

sudo apt-get -y autoremove r-bioc-sva

Remove r-bioc-sva Configurations and Data

To remove r-bioc-sva configuration and data from Debian 12 we can use the following command:

sudo apt-get -y purge r-bioc-sva

Remove r-bioc-sva configuration, data, and all of its dependencies

We can use the following command to remove r-bioc-sva configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge r-bioc-sva

Dependencies

r-bioc-sva have the following dependencies:

References

Summary

In this tutorial we learn how to install r-bioc-sva package on Debian 12 using different package management tools: apt, apt-get and aptitude.