ttgsea

DOI: 10.18129/B9.bioc.ttgsea    

This is the development version of ttgsea; to use it, please install the devel version of Bioconductor.

Tokenizing Text of Gene Set Enrichment Analysis

Bioconductor version: Development (3.13)

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")

 

HTML R Script ttgsea
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneExpression, GeneSetEnrichment, Software
Version 0.99.23
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

Follow Installation instructions to use this package in your R session.

Source Package ttgsea_0.99.23.tar.gz
Windows Binary ttgsea_0.99.23.zip (32- & 64-bit)
macOS 10.13 (High Sierra) ttgsea_0.99.23.tgz
Source Repository git clone https://git.bioconductor.org/packages/ttgsea
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ttgsea
Package Short Url https://bioconductor.org/packages/ttgsea/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: