transomics2cytoscape.Rmd

---
title: "transomics2cytoscape"
author: "Kozo Nishida"
date: "2/26/2020"
package: transomics2cytoscape
output:
    BiocStyle::html_document
vignette: |
    %\VignetteIndexEntry{transomics2cytoscape}
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## Introduction

To understand transomics datasets, [Yugi et al. 2014](https://pubmed.ncbi.nlm.nih.gov/25131207) has proposed a method for network visualization by integrating multiple pathways in 3D space.
The 3D network visualization was created by [VANTED](https://pubmed.ncbi.nlm.nih.gov/23140568) and human operation.

[RIKEN Plant Metabolome MetaDatabase (RPMM)](http://metabobank.riken.jp/) is 
used to provide integrated plant metabolome data generated by RIKEN. 
The database provides data in the bases of standardized metadata techniques 
including semantic web and Resource Description Framework (RDF). 
The rRPMM package is an accessor for RPMM.

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