Package: TissueEnrich
Type: Package
Title: Tissue-specific gene enrichment analysis
Version: 1.31.0
Authors@R: c(person("Ashish Jain",
        email="jain.ashishjain1@gmail.com",
        role=c("aut", "cre")), person("Geetu Tuteja",
        email="geetu@iastate.edu",
        role=c("aut")))
Description: 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.
License: MIT + file LICENSE
VignetteBuilder: knitr
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
Suggests: knitr, rmarkdown, testthat
Encoding: UTF-8
RoxygenNote: 7.3.1
biocViews: GeneSetEnrichment, GeneExpression, Sequencing
Config/pak/sysreqs: libicu-dev libpng-dev libxml2-dev libssl-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:44:14 UTC
RemoteUrl: https://github.com/bioc/TissueEnrich
RemoteRef: HEAD
RemoteSha: 706448a559012f61efa1f0537e641291116102b0
NeedsCompilation: no
Packaged: 2026-01-22 20:51:19 UTC; root
Author: Ashish Jain [aut, cre],
  Geetu Tuteja [aut]
Maintainer: Ashish Jain <jain.ashishjain1@gmail.com>
Built: R 4.6.0; ; 2026-01-22 20:53:16 UTC; windows
