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RbioRXN (version 1.5.1)

Process Rhea, KEGG, MetaCyc, Unipathway Biochemical Reaction Data

Description

To facilitate 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

1.5.1

License

GPL (>= 2)

Maintainer

Byoungnam Min

Last Published

May 19th, 2015

Functions in RbioRXN (1.5.1)

instantiate.rhea

Instantiate Rhea generic reaction
get.kegg.all

Download current KEGG REACTION and KEGG COMPOUND database using KEGGREST package
example

Rbiorxn example data
is.generic.rhea

Check given reaction is generic reaction
get.unipathway.all

Download current Unipathway
is.generic.metacyc

Check given reaction is generic reaction
check.mass.balance

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

Download given KEGG REACTION entry using KEGGREST package
RbioRXN-package

RbioRXN - Process Rhea, KEGG, MetaCyc, Unipathway Biochemical Reaction Data
get.metacyc.reaction.byId

Download given MetaCyc reaction via BioCyc web services
get.rhea.all

Download current Rhea in data.frame() object
get.rhea.byId

Download Rhea by Rhea ID
parse.metacyc.compound

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

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

Download and parse current ChEBI
get.rhea.byCompound

Download Rhea reaction by compound
get.metacyc.all

Download current MetaCyc via BioCyc Web Services
build.subtable

Build sub-table for the entries with multiple values
instantiate.metacyc

Instantiate MetaCyc generic reaction
example

Rbiorxn example data