Bioconductor – ttgsea (development version)

DOI: 10.18129/B9.bioc.ttgsea  

 

This is the development version of ttgsea; for the stable release version, see
ttgsea.

Tokenizing Text of Gene Set Enrichment Analysis

Bioconductor version: Development (3.14)

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.

Author: Dongmin Jung [cre, aut]

Maintainer: Dongmin Jung <dmdmjung at gmail.com>

Citation (from within R,
enter citation("ttgsea")):

Installation

To install this package, start R (version
“4.1”) and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ttgsea")

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("ttgsea")

 

Details

biocViews GeneExpression, GeneSetEnrichment, Software
Version 1.1.0
In Bioconductor since BioC 3.13 (R-4.1) (
License Artistic-2.0
Depends keras
Imports tm, text2vec, tokenizers, textstem, stopwords, data.table, purrr, DiagrammeR, stats
LinkingTo
Suggests fgsea, knitr, testthat, reticulate, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me DeepPINCS
Suggests Me
Links To Me
Build Report  

Package Archives

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Installation
instructions to use this
package in your R session.


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