How To Install r-bioc-qusage on Kali Linux
Introduction
In this tutorial we learn how to install r-bioc-qusage on Kali Linux.
What is r-bioc-qusage
r-bioc-qusage is:
This package is an implementation the Quantitative Set Analysis for Gene Expression (QuSAGE) method described in (Yaari G. et al, Nucl Acids Res, 2013). This is a novel Gene Set Enrichment-type test, which is designed to provide a faster, more accurate, and easier to understand test for gene expression studies. qusage accounts for inter-gene correlations using the Variance Inflation Factor technique proposed by Wu et al. (Nucleic Acids Res, 2012). In addition, rather than simply evaluating the deviation from a null hypothesis with a single number (a P value), qusage quantifies gene set activity with a complete probability density function (PDF). From this PDF, P values and confidence intervals can be easily extracted. Preserving the PDF also allows for post-hoc analysis (e.g., pair-wise comparisons of gene set activity) while maintaining statistical traceability. Finally, while qusage is compatible with individual gene statistics from existing methods (e.g., LIMMA), a Welch-based method is implemented that is shown to improve specificity. For questions, contact Chris Bolen ([email protected]) or Steven Kleinstein ([email protected])
There are three methods to install r-bioc-qusage on Kali Linux. 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-qusage Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get updateAfter updating apt database, We can install r-bioc-qusage using apt-get by running the following command:
sudo apt-get -y install r-bioc-qusageInstall r-bioc-qusage Using apt
Update apt database with apt using the following command.
sudo apt updateAfter updating apt database, We can install r-bioc-qusage using apt by running the following command:
sudo apt -y install r-bioc-qusageInstall r-bioc-qusage Using aptitude
If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.
sudo aptitude updateAfter updating apt database, We can install r-bioc-qusage using aptitude by running the following command:
sudo aptitude -y install r-bioc-qusageHow To Uninstall r-bioc-qusage on Kali Linux
To uninstall only the r-bioc-qusage package we can use the following command:
sudo apt-get remove r-bioc-qusageUninstall r-bioc-qusage And Its Dependencies
To uninstall r-bioc-qusage and its dependencies that are no longer needed by Kali Linux, we can use the command below:
sudo apt-get -y autoremove r-bioc-qusageRemove r-bioc-qusage Configurations and Data
To remove r-bioc-qusage configuration and data from Kali Linux we can use the following command:
sudo apt-get -y purge r-bioc-qusageRemove r-bioc-qusage configuration, data, and all of its dependencies
We can use the following command to remove r-bioc-qusage configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-bioc-qusageDependencies
r-bioc-qusage have the following dependencies:
References
Summary
In this tutorial we learn how to install r-bioc-qusage package on Kali Linux using different package management tools: apt, apt-get and aptitude.