RbioRXN v1.3.1
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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 |
| depends | base (>= 3.0.3) , fmcsR , R (>= 3.0.3) |
| imports | data , data.table , gdata , KEGGREST , plyr , RCurl , stringr |
| Contributors | Byeonghyuk Park, Byoungnam Min, Kyoung Kim, In-Geol Choi |
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[](http://www.rdocumentation.org/packages/RbioRXN)