How to Install and Uninstall r-bioc-qusage Package on Ubuntu 20.10 (Groovy Gorilla)

Last updated: November 26,2024

1. Install "r-bioc-qusage" package

Please follow the guidance below to install r-bioc-qusage on Ubuntu 20.10 (Groovy Gorilla)


    
        
            $
        

        
            
                sudo apt update
            
                    
    
    Copied


    
        
            $
        

        
            
                sudo apt install
            
                        
                r-bioc-qusage
            
                    
    
    Copied

2. Uninstall "r-bioc-qusage" package

This is a short guide on how to uninstall r-bioc-qusage on Ubuntu 20.10 (Groovy Gorilla):


    
        
            $
        

        
            
                sudo apt remove
            
                        
                r-bioc-qusage
            
                    
    
    Copied


    
        
            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
    Copied

3. Information about the r-bioc-qusage package on Ubuntu 20.10 (Groovy Gorilla)

Package: r-bioc-qusage
Architecture: all
Version: 2.22.0-1build1
Priority: optional
Section: universe/gnu-r
Origin: Ubuntu
Maintainer: Ubuntu Developers
Original-Maintainer: Debian R Packages Maintainers
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Installed-Size: 10032
Depends: r-base-core (>= 4.0.0.20200528-1), r-api-4.0, r-api-bioc-3.11, r-bioc-limma (>= 3.14), r-bioc-biobase, r-cran-nlme, r-cran-emmeans, r-cran-fftw
Filename: pool/universe/r/r-bioc-qusage/r-bioc-qusage_2.22.0-1build1_all.deb
Size: 9999900
MD5sum: d807db108e86ed59e0fa43ff618cb73f
SHA1: 659c4c3b710e34255b2bf2de8f4833a7b0578d25
SHA256: 2b3d9048c4c9087649891fdbebad145084279f79ac5fb6bcebba2b357bf80b86
SHA512: 5d8b66d73c80938fa820379f74abca2776c523ed2b974ea2245e002456fa1b1e19542fba7a0465627b812081098b72dec464f58c043858d97dc13a2a56cb01f5
Homepage: https://bioconductor.org/packages/qusage/
Description-en: qusage: Quantitative Set Analysis for Gene Expression
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])
Description-md5: a627382dbaa3db9171d4e40dcffc4197