RbioRXN: Process Rhea, KEGG, MetaCyc, Unipathway Biochemical Reaction Data

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.

Author
Byoungnam Min, Byeonghyeok Park, Kyoung Heon Kim and In-Geol Choi
Date of publication
2015-05-19 13:07:25
Maintainer
Byoungnam Min <mbnmbn00@gmail.com>
License
GPL (>= 2)
Version
1.5.1

View on CRAN

Man pages

build.subtable
Build sub-table for the entries with multiple values
check.mass.balance
Check given biochemical reaction is mass-balanced
example
Rbiorxn example data
get.chebi.all
Download and parse current ChEBI
get.kegg.all
Download current KEGG REACTION and KEGG COMPOUND database...
get.kegg.byId
Download given KEGG REACTION entry using KEGGREST package
get.metacyc.all
Download current MetaCyc via BioCyc Web Services
get.metacyc.reaction.byId
Download given MetaCyc reaction via BioCyc web services
get.rhea.all
Download current Rhea in data.frame() object
get.rhea.byCompound
Download Rhea reaction by compound
get.rhea.byId
Download Rhea by Rhea ID
get.unipathway.all
Download current Unipathway
instantiate.metacyc
Instantiate MetaCyc generic reaction
instantiate.rhea
Instantiate Rhea generic reaction
is.generic.metacyc
Check given reaction is generic reaction
is.generic.rhea
Check given reaction is generic reaction
parse.metacyc.compound
Parse MetaCyc compound data (compounds.dat in attribute-value...
parse.metacyc.reaction
Parse MetaCyc reaction data (reactions.dat in attribute-value...
RbioRXN-package
RbioRXN - Process Rhea, KEGG, MetaCyc, Unipathway Biochemical...

Files in this package

RbioRXN
RbioRXN/NAMESPACE
RbioRXN/data
RbioRXN/data/example.rda
RbioRXN/R
RbioRXN/R/get.metacyc.reaction.byId.R
RbioRXN/R/instantiate.R
RbioRXN/R/RbioRXN-internal.R
RbioRXN/R/get.metacyc.all.R
RbioRXN/R/check.mass.balance.R
RbioRXN/R/get.rhea.byCompound.R
RbioRXN/R/build.subtable.R
RbioRXN/R/instantiate.metacyc.R
RbioRXN/R/is.generic.rhea.R
RbioRXN/R/get.rhea.byId.R
RbioRXN/R/instantiate.rhea.R
RbioRXN/R/parse.metacyc.reaction.R
RbioRXN/R/get.kegg.byId.R
RbioRXN/R/is.generic.metacyc.R
RbioRXN/R/get.kegg.all.R
RbioRXN/R/parse.metacyc.compound.R
RbioRXN/R/get.rhea.all.R
RbioRXN/R/get.unipathway.all.R
RbioRXN/R/get.chebi.all.R
RbioRXN/MD5
RbioRXN/DESCRIPTION
RbioRXN/man
RbioRXN/man/get.unipathway.all.Rd
RbioRXN/man/get.chebi.all.Rd
RbioRXN/man/is.generic.metacyc.Rd
RbioRXN/man/get.rhea.byCompound.Rd
RbioRXN/man/parse.metacyc.reaction.Rd
RbioRXN/man/parse.metacyc.compound.Rd
RbioRXN/man/get.kegg.all.Rd
RbioRXN/man/instantiate.metacyc.Rd
RbioRXN/man/get.kegg.byId.Rd
RbioRXN/man/check.mass.balance.Rd
RbioRXN/man/get.metacyc.reaction.byId.Rd
RbioRXN/man/is.generic.rhea.Rd
RbioRXN/man/get.metacyc.all.Rd
RbioRXN/man/get.rhea.all.Rd
RbioRXN/man/example.Rd
RbioRXN/man/get.rhea.byId.Rd
RbioRXN/man/instantiate.rhea.Rd
RbioRXN/man/RbioRXN-package.Rd
RbioRXN/man/build.subtable.Rd