How to Install and Uninstall r-bioc-qusage Package on Ubuntu 21.10 (Impish Indri)

Last updated: May 19,2024

1. Install "r-bioc-qusage" package

In this section, we are going to explain the necessary steps to install r-bioc-qusage on Ubuntu 21.10 (Impish Indri)


    
        
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                sudo apt update
            
                    
    
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            $
        

        
            
                sudo apt install
            
                        
                r-bioc-qusage
            
                    
    
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2. Uninstall "r-bioc-qusage" package

This guide let you learn how to uninstall r-bioc-qusage on Ubuntu 21.10 (Impish Indri):


    
        
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                sudo apt remove
            
                        
                r-bioc-qusage
            
                    
    
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            $
        

        
            
                sudo apt autoclean && sudo apt autoremove
            
                    
    
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3. Information about the r-bioc-qusage package on Ubuntu 21.10 (Impish Indri)

Package: r-bioc-qusage
Architecture: all
Version: 2.24.0-1
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 (>= 4.0.2-1build1), r-api-4.0, r-api-bioc-3.12, 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_2.24.0-1_all.deb
Size: 9999560
MD5sum: 9870b1e8781bf9c10c5cb4a0b272d206
SHA1: fdaa89ff0168e16dceb9fa3990f3fcdc563f88bd
SHA256: 9d21b1f0f6c885b7564929d7810b8ffa3d1dc72e50d21319abd51c9c79d6ced9
SHA512: 92e90ab30a59c5bdd2857b69f57e7a91c508680e3655f3cb61a48073a6e3fa6763342c7a9863bdf74ef2bcf1c81f5fc8c95157cb7239fe5aef988368925a3b8e
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