How To Install r-bioc-sva on Ubuntu 22.04
Introduction
In this tutorial we learn how to install r-bioc-sva
on Ubuntu 22.04.
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 Ubuntu 22.04. 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 Ubuntu. 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 Ubuntu 22.04
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 Ubuntu 22.04, 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 Ubuntu 22.04 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
References
Summary
In this tutorial we learn how to install r-bioc-sva
package on Ubuntu 22.04 using different package management tools: apt
, apt-get
and aptitude
.