Package: ttgsea
Type: Package
Title: Tokenizing Text of Gene Set Enrichment Analysis
Description: Functional enrichment analysis methods such as gene set
        enrichment analysis (GSEA) have been widely used for analyzing
        gene expression data. GSEA is a powerful method to infer
        results of gene expression data at a level of gene sets by
        calculating enrichment scores for predefined sets of genes.
        GSEA depends on the availability and accuracy of gene sets.
        There are overlaps between terms of gene sets or categories
        because multiple terms may exist for a single biological
        process, and it can thus lead to redundancy within enriched
        terms. In other words, the sets of related terms are
        overlapping. Using deep learning, this pakage is aimed to
        predict enrichment scores for unique tokens or words from text
        in names of gene sets to resolve this overlapping set issue.
        Furthermore, we can coin a new term by combining tokens and
        find its enrichment score by predicting such a combined tokens.
Version: 1.20.0
Date: 2021-11-12
Authors@R: c(person(given="Dongmin", family="Jung", email="dmdmjung@gmail.com", role=c("cre", "aut"), comment = c(ORCID = "0000-0001-7499-8422")))
Depends: keras
Imports: tm, text2vec, tokenizers, textstem, stopwords, data.table,
        purrr, DiagrammeR, stats
Suggests: fgsea, knitr, testthat, reticulate, rmarkdown
SystemRequirement: tensorflow
License: Artistic-2.0
biocViews: Software, GeneExpression, GeneSetEnrichment
NeedsCompilation: no
VignetteBuilder: knitr
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libpng-dev
        libuv1-dev libxml2-dev python3 libx11-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:54:38 UTC
RemoteUrl: https://github.com/bioc/ttgsea
RemoteRef: RELEASE_3_23
RemoteSha: f8d111c225df0202b304634269a13d7a11ff0edd
Packaged: 2026-04-30 07:01:21 UTC; root
Author: Dongmin Jung [cre, aut] (ORCID:
    <https://orcid.org/0000-0001-7499-8422>)
Maintainer: Dongmin Jung <dmdmjung@gmail.com>
Built: R 4.6.0; ; 2026-04-30 08:22:07 UTC; unix
