gsean-package {gsean} | R Documentation

## Gene Set Enrichment Analysis with Networks

### Description

Biological molecules in a living organism seldom work individually. They usually interact each other in a cooperative way. Biological process is too complicated to understand without considering such interactions. Thus, network-based procedures can be seen as powerful methods for studying complex process. However, many methods are devised for analyzing individual genes. It is said that techniques based on biological networks such as gene co-expression are more precise ways to represent information than those using lists of genes only. This package is aimed to integrate the gene expression and biological network. A biological network is constructed from gene expression data and it is used for Gene Set Enrichment Analysis.

### Details

The DESCRIPTION file:

Package: | gsean
Type: | Package
Title: | Gene Set Enrichment Analysis with Networks
Description: | Biological molecules in a living organism seldom work individually. They usually interact each other in a cooperative way. Biological process is too complicated to understand without considering such interactions. Thus, network-based procedures can be seen as powerful methods for studying complex process. However, many methods are devised for analyzing individual genes. It is said that techniques based on biological networks such as gene co-expression are more precise ways to represent information than those using lists of genes only. This package is aimed to integrate the gene expression and biological network. A biological network is constructed from gene expression data and it is used for Gene Set Enrichment Analysis.
Version: | 1.0.0
Date: | 2018-01-24
Author: | Dongmin Jung
Maintainer: | Dongmin Jung <dmdmjung@gmail.com>
Depends: | R (>= 3.5), fgsea, PPInfer
Suggests: | DESeq2, knitr, plotly, RANKS, WGCNA
License: | Artistic-2.0
biocViews: | Software, StatisticalMethod, Network, GraphAndNetwork, GeneSetEnrichment, GeneExpression, NetworkEnrichment, Pathways, DifferentialExpression
NeedsCompilation: | no
VignetteBuilder: | knitr

Index of help topics:

    GO_dme                  Gene Ontology terms with gene ID for Drosophila
                            melanogaster
    KEGG_hsa                KEGG pathways with gene symbol for human
    centrality_gsea         Gene Set Enrichment Analysis with centrality
                            measure
    exprs2adj               Convert gene expression data to adjacency
                            matrix by using correlation coefficients
    gsean                   Gene Set Enrichment Analysis with Networks
    gsean-package           Gene Set Enrichment Analysis with Networks
    label_prop_gsea         Over-representaion analysis with the label
                            propagation algorithm

### Author(s)

Dongmin Jung

Maintainer: Dongmin Jung <dmdmjung@gmail.com>

[Package gsean version 1.0.0 Index]