goSorensen
This is the released version of goSorensen; for the devel version, see goSorensen.
Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)
Bioconductor version: Release (3.23)
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("goSorensen")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 goSorensen R-Package | HTML | R Script |
| Working with te Irrelevance-threshold Matrix of Dissimilarities. | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, Clustering, GO, GeneExpression, GeneSetEnrichment, GraphAndNetwork, KEGG, Microarray, MultipleComparison, Pathways, Reactome, Software |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | GPL-3 |
| Depends | R (>= 4.4) |
| Imports | clusterProfiler, goProfiles, org.Hs.eg.db, parallel, stats, stringr |
| System Requirements | |
| URL |
See More
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | goSorensen_1.14.0.tar.gz |
| Windows Binary (x86_64) | goSorensen_1.14.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | goSorensen_1.14.0.tgz |
| macOS Binary (sonoma-arm64) | goSorensen_1.14.0.tgz |
| 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 |