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RbioRXN (version 1.3.1)

RbioRXN - process Rhea, KEGG, MetaCyc, Unipathway biochemical reaction data

Description

RbioRXN is an R package that facilitates retrieving and processing biochemical reaction data such as Rhea, MetaCyc, KEGG and Unipathway. The package provides the functions to download and parse data, instantiate generic reaction and check mass-balance. The package aims to construct an integrated metabolic network and genome-scale metabolic model.

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Version

Install

install.packages('RbioRXN')

Monthly Downloads

42

Version

1.3.1

License

GPL (>= 2)

Maintainer

Byoungnam Min

Last Published

July 30th, 2014

Functions in RbioRXN (1.3.1)

get.rhea.byId

Download Rhea by Rhea ID
get.rhea.byCompound

Download Rhea reaction by compound
check.mass.balance

Check given biochemical reaction is mass-balanced
get.kegg.byId

Download given KEGG REACTION entry using KEGGREST package
get.unipathway.all

Download current Unipathway
build.subtable

Build sub-table for the entries with multiple values
get.kegg.all

Download current KEGG REACTION and KEGG COMPOUND database using KEGGREST package
instantiate.rhea

Instantiate Rhea generic reaction
RbioRXN-package

RbioRXN - Download/process Rhea, MetaCyc, KEGG and UniPathway biochemical reaction
example

Rbiorxn example data
get.metacyc.all

Download current MetaCyc via BioCyc Web Services
get.rhea.all

Download current Rhea in data.frame() object
is.generic.metacyc

Check given reaction is generic reaction
instantiate.metacyc

Instantiate MetaCyc generic reaction
get.chebi.all

Download and parse current ChEBI
parse.metacyc.compound

Parse MetaCyc compound data (compounds.dat in attribute-value format)
get.metacyc.reaction.byId

Download given MetaCyc reaction via BioCyc web services
is.generic.rhea

Check given reaction is generic reaction
parse.metacyc.reaction

Parse MetaCyc reaction data (reactions.dat in attribute-value format)