goSorensen

DOI: 10.18129/B9.bioc.goSorensen    

This is the development version of goSorensen; for the stable release version, see goSorensen.

Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

Bioconductor version: Development (3.17)

This package implements inferential methods to compare gene lists (in this first release, to prove equivalence) in terms of their biological meaning as expressed in the GO. The compared gene lists are characterized by cross-tabulation frequency tables of enriched GO items. Dissimilarity between gene lists is evaluated using the Sorensen-Dice index. The fundamental guiding principle is that two gene lists are taken as similar if they share a great proportion of common enriched GO items.

Author: Pablo Flores [aut, cre] , Jordi Ocana [aut, ctb] (0000-0002-4736-699), Alexandre Sanchez-Pla [ctb] , Miquel Salicru [ctb]

Maintainer: Pablo Flores <p_flores at espoch.edu.ec>

Citation (from within R, enter citation("goSorensen")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("goSorensen")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("goSorensen")

 

HTML R Script An introduction to equivalence test between feature lists using goSorensen.
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, Clustering, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, KEGG, Microarray, MultipleComparison, Pathways, Reactome, Software
Version 1.1.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License GPL-3
Depends R (>= 4.2.0)
Imports GO.db, org.Hs.eg.db, goProfiles, stats, clusterProfiler, parallel
LinkingTo
Suggests BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package goSorensen_1.1.0.tar.gz
Windows Binary goSorensen_1.1.0.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/goSorensen
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/goSorensen
Package Short Url https://bioconductor.org/packages/goSorensen/
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