About MetQy and installation

MetQy - metabolic query

MetQy is a R package to ease interfacing with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to query metabolic functions of genes and genomes. As discussed in detail in the associated paper (see above), MetQy can be used to convert key parts of the data contained in the KEGG database into R data structures, and perform analyses on this data.

Using MetQy

CITE US

Please cite:

    Andrea Martinez-Vernon, Fred Farrell, Orkun Soyer. MetQy: an R package to query metabolic functions of genes and genomes. 
        bioRxiv - https://www.biorxiv.org/content/early/2017/11/16/215525

https://www.biorxiv.org/content/early/2017/11/16/215525

Commercial use

MetQy is a free software for academic purposes. If interested in commercial use, please read the LICENCE and contact Warwick Ventures

Installation

There are two ways of installing the package:

1. Run the following command within the R environment. Requires package devtools

   # install.packages("devtools") # Uncomment if not previously installed 
   
   # Install MetQy - required dependent packages are installed automatically
   devtools::install_github('OSS-Lab/MetQy',subdir = 'MetQy_1.1.0',dependencies = TRUE) # 
   

2. Download 'MetQy_1.1.0.tar.gz' and run the following commands within the R environment:

   # Manually install dependent packages - remove any that is already installed. Installing will replace local library.
   install.packages(c("dplyr","ggplot2","gsubfn","reshape2","xtable"))
   
   # Install MetQy
   install.packages('<path_to_directory>/MetQy_1.1.0.tar.gz',repos=NULL)
   library(MetQy)
   

3. Download 'MetQy_1.1.0.tgz' and run the following commands within the R environment:

   ## Note that this option might only be compatible with OS X. 
   
   # Manually install dependent packages - remove any that is already installed. Installing will replace local library.
   install.packages(c("dplyr","ggplot2","gsubfn","reshape2","xtable"))
   
   # Install MetQy
   install.packages('<path_to_directory>/MetQy_1.1.0.tgz',repos=NULL)  # QUICKER
   library(MetQy)
   

Use of KEGG data

MetQy contains in-built KEGG data (downloaded 20/02/2018) which is hidden from the user, in compliance with the KEGG FTP licence. Users with FTP access can use the parsing functions to process the KEGG database files and to provide up-to-date information to the query functions.

For more information and usage examples visit the links below.