RbioRXN v1.3.1

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by Byoungnam Min

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

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.

Functions in RbioRXN

Name Description
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)
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Details

Type Package
Date 2014-07-30
License GPL (>= 2)
Packaged 2014-07-30 06:22:26 UTC; mbnmbn00
NeedsCompilation no
Repository CRAN
Date/Publication 2014-07-30 08:59:13

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