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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>

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

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

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) (1.5 years)
License GPL-3
Depends R (>= 4.3.0)
Imports GO.db, org.Hs.eg.db, goProfiles, stats, clusterProfiler, parallel, stringr
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Suggests BiocStyle, knitr, rmarkdown
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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) goSorensen_1.5.0.tgz
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/
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