goseq

This is the released version of goseq; for the devel version, see goseq.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6

Gene Ontology analyser for RNA-seq and other length biased data

Bioconductor version: Release (3.23)

Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.

Author: Matthew Young [aut], Nadia Davidson [aut], Federico Marini [ctb, cre] ORCID: 0000-0003-3252-7758

Maintainer: Federico Marini <marinif at uni-mainz.de>

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

Matthew Young, Nadia Davidson. goseq: Gene Ontology analyser for RNA-seq and other length biased data. doi:10.18129/B9.bioc.goseq, R package version 1.64.0, https://bioconductor.org/packages/goseq.

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")

BiocManager::install("goseq")

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("goseq")

goseq User's Guide	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, ImmunoOncology, KEGG, Pathways, RNASeq, Sequencing, Software, Transcription
Version	1.64.0
In Bioconductor since	BioC 2.6 (R-2.11) (16.5 years)
License	LGPL (>= 2)
Depends	R (>= 2.11.0), BiasedUrn, geneLenDataBase (>= 1.9.2)
Imports	mgcv, graphics, stats, utils, AnnotationDbi, GO.db, BiocGenerics, methods, rtracklayer, GenomicFeatures, Seqinfo
System Requirements
URL	https://github.com/federicomarini/goseq
Bug Reports	https://github.com/federicomarini/goseq/issues

Suggests	edgeR, org.Hs.eg.db
Linking To
Enhances
Depends On Me	rgsepd
Imports Me	ChAMP, Damsel, ideal, mosdef, SMITE
Suggests Me	carnation, sparrow
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	goseq_1.64.0.tar.gz
Windows Binary (x86_64)	goseq_1.64.0.zip
macOS Binary (big-sur-x86_64)	goseq_1.64.0.tgz
macOS Binary (sonoma-arm64)	goseq_1.64.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/goseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/goseq
Package Short Url	https://bioconductor.org/packages/goseq/
Package Downloads Report	Download Stats