ttgsea
Tokenizing Text of Gene Set Enrichment Analysis
Bioconductor version: Release (3.17)
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("ttgsea")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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")| ttgsea | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneSetEnrichment, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (2 years) |
| License | Artistic-2.0 |
| Depends | keras |
| Imports | tm, text2vec, tokenizers, textstem, stopwords, data.table, purrr, DiagrammeR, stats |
| Linking To | |
| Suggests | fgsea, knitr, testthat, reticulate, rmarkdown |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | |
| Imports Me | DeepPINCS, GenProSeq |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ttgsea_1.8.0.tar.gz |
| Windows Binary | ttgsea_1.8.0.zip |
| macOS Binary (x86_64) | ttgsea_1.8.0.tgz |
| macOS Binary (arm64) | ttgsea_1.8.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ttgsea |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ttgsea |
| Bioc Package Browser | https://code.bioconductor.org/browse/ttgsea/ |
| Package Short Url | https://bioconductor.org/packages/ttgsea/ |
| Package Downloads Report | Download Stats |