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>
citation("TissueEnrich")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| TissueEnrich | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Sequencing, Software |
| Version | 1.4.1 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, testthat |
| 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 | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/TissueEnrich/ |
| Package Short Url | https://bioconductor.org/packages/TissueEnrich/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |