TissueEnrich
Tissue-specific gene enrichment analysis
Bioconductor version: 3.24 · Package version: 1.33.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TissueEnrich")Details
| Maintainer | Ashish Jain <jain.ashishjain1@gmail.com> |
| Author | Ashish Jain [aut, cre], Geetu Tuteja [aut] |
| License | MIT + file LICENSE |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, GeneSetEnrichment, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/TissueEnrich/ |
Citation
From within R, enter citation("TissueEnrich"):
Ashish Jain, Geetu Tuteja. TissueEnrich: Tissue-specific gene enrichment analysis. doi:10.18129/B9.bioc.TissueEnrich, R package version 1.33.0, https://bioconductor.org/packages/TissueEnrich.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | TissueEnrich_1.33.0.tar.gz |
| Windows binary (x86_64) | TissueEnrich_1.33.0.zip |
| macOS binary (arm64) | TissueEnrich_1.33.0.tgz |
| macOS binary (x86_64) | TissueEnrich_1.33.0.tgz |
Dependencies
Depends: R (>= 3.5), ggplot2 (>= 2.2.1), SummarizedExperiment (>= 1.6.5), GSEABase (>= 1.38.2)
Imports: dplyr (>= 0.7.3), tidyr (>= 0.8.0), stats