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 (3.19)

This package implements inferential methods to compare gene lists 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>

Installation

To install this package, start R (version "4.4") 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	1.5.0
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
License	GPL-3
Depends	R (>= 4.3.0)
Imports	GO.db, org.Hs.eg.db, goProfiles, stats, clusterProfiler, parallel, stringr
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	goSorensen_1.5.0.tar.gz
Windows Binary	goSorensen_1.5.0.zip
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
Bioc Package Browser	https://code.bioconductor.org/browse/goSorensen/
Package Short Url	https://bioconductor.org/packages/goSorensen/
Package Downloads Report	Download Stats