TissueEnrich

DOI: 10.18129/B9.bioc.TissueEnrich    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see TissueEnrich.

Tissue-specific gene enrichment analysis

Bioconductor version: 3.9

The TissueEnrich package is used to calculate enrichment of tissue-specific genes in a set of input genes. For example, the user can input the most highly expressed genes from RNA-Seq data, or gene co-expression modules to determine which tissue-specific genes are enriched in those datasets. Tissue-specific genes were defined by processing RNA-Seq data from the Human Protein Atlas (HPA) (Uhlén et al. 2015), GTEx (Ardlie et al. 2015), and mouse ENCODE (Shen et al. 2012) using the algorithm from the HPA (Uhlén et al. 2015).The hypergeometric test is being used to determine if the tissue-specific genes are enriched among the input genes. Along with tissue-specific gene enrichment, the TissueEnrich package can also be used to define tissue-specific genes from expression datasets provided by the user, which can then be used to calculate tissue-specific gene enrichments.

Author: Ashish Jain [aut, cre], Geetu Tuteja [aut]

Maintainer: Ashish Jain <jain at iastate.edu>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("TissueEnrich")

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("TissueEnrich")

 

HTML	R Script	TissueEnrich
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneExpression, GeneSetEnrichment, Sequencing, Software
Version	1.4.1
In Bioconductor since	BioC 3.7 (R-3.5) (1.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.5), ensurer (>= 1.1.0), ggplot2 (>= 2.2.1), tidyr (>= 0.8.0), SummarizedExperiment(>= 1.6.5), GSEABase(>= 1.38.2)
Imports	dplyr (>= 0.7.3), stats
LinkingTo
Suggests	knitr, rmarkdown, testthat
SystemRequirements
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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	TissueEnrich_1.4.1.tar.gz
Windows Binary	TissueEnrich_1.4.1.zip
Mac OS X 10.11 (El Capitan)	TissueEnrich_1.4.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TissueEnrich
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/TissueEnrich
Package Short Url	https://bioconductor.org/packages/TissueEnrich/
Package Downloads Report	Download Stats