goSorensen

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16

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

Bioconductor version: Development (3.24)

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] ORCID: 0000-0002-7156-8547 , Jordi Ocana [aut, ctb] ORCID: 0000-0002-4736-6996 , Alex Mantilla [aut, ctb] ORCID: 0000-0001-7047-7072 , Alexandre Sanchez-Pla [ctb] ORCID: 0000-0002-8673-7737 , Miquel Salicru [ctb] ORCID: 0000-0001-9644-5626

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

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

Pablo Flores, Jordi Ocana, Alex Mantilla. goSorensen: Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO). doi:10.18129/B9.bioc.goSorensen, R package version 1.15.0, https://bioconductor.org/packages/goSorensen.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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")

Working with te Irrelevance-threshold Matrix of Dissimilarities.	HTML	R Script
An Introduction to goSorensen R-Package	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Clustering, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, KEGG, Microarray, MultipleComparison, Pathways, Reactome, Software
Version	1.15.0
In Bioconductor since	BioC 3.16 (R-4.2) (4 years)
License	GPL-3
Depends	R (>= 4.5)
Imports	clusterProfiler, goProfiles, parallel, stats, stringr, withr
System Requirements
URL	https://github.com/pablof1988/goSorensen
Bug Reports	https://github.com/pablof1988/goSorensen/issues

Suggests	BiocManager, BiocStyle, knitr, rmarkdown, org.At.tair.db, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.EcSakai.eg.db, org.EcK12.eg.db, org.Gg.eg.db, org.Mm.eg.db, org.Mmu.eg.db, org.Rn.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Pt.eg.db, org.Xl.eg.db, GO.db, ggplot2, ggrepel, DT, magick, AnnotationDbi, org.Hs.eg.db
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	goSorensen_1.15.0.tar.gz
Windows Binary (x86_64)	goSorensen_1.15.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	goSorensen_1.15.0.tgz
macOS Binary (sonoma-arm64)	goSorensen_1.15.0.tgz
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/
Package Downloads Report	Download Stats