mmnet: A metagenomic pipeline for systems biology

This package gives the implementations microbiome metabolic network constructing and analyzing. It introduces a unique metagenomic systems biology approach, mapping metagenomic data to the KEGG global metabolic pathway and constructing a systems-level network. The system-level network and the next topological analysis will be of great help to analysis the various functional properties, including regulation and metabolic functionality of the metagenome.

Author
Yang Cao, Fei Li
Date of publication
None
Maintainer
Yang Cao <yiluheihei@gmail.com>, Fei Li <pittacus@gmail.com>
License
GPL (>= 2)
Version
1.12.0

View on Bioconductor

Man pages

anno
annotation profile of two sample data sets
checkMgrastMetagenome
Check whether the MGRAST annotation is completed
constructMetabolicNetwork
Metabolic network construction of microbiome
constructSSN
construct the state specific network
delMgrastInbox
Delete the files in you MG-RAST inbox
differentialAnalyzeNet
the KO difference abundance of specific state
estimateAbundance
Getting KO (KEGG ontology) and abundance information
generateMgrastWebkey
Generate your webkey on MGRAST
generateMgrastWebsession
Generate your websession
getKOPathwayInfo
Get the KEGG metabolic pathway information
getMgrastAnnotation
Get the annotation profile from MGRAST
listMgrastInbox
List the contents of the user inbox
listMgrastProject
List all the private projects you summitted to MGRAST
loadMetabolicData
Metabolic data loading
loginMgrast
Login to the MGRAST
mmnet-package
A metagenomic pipeline for systems biology
preprocessKOMetabolites
Preprocessing of KO's (enzyme's) metabolites
RefDbcache
Reference data for global metabolic construction
saveMetabolicData
Save a new version of the reference metabolic data
showMetagenomicNet
Visualiation of metabolic network
submitMgrastJob
Create a job on MGRAST
topologicalAnalyzeNet
Analyze the specific state network
updateKEGGPathway
Updating and saving the reference (KEGG metabolic pathway)...
uploadMgrast
Upload your sequence to MGRAST

Files in this package

mmnet/.BBSoptions
mmnet/DESCRIPTION
mmnet/NAMESPACE
mmnet/R
mmnet/R/BIOM-class.R
mmnet/R/IO-methods.R
mmnet/R/allClasses.R
mmnet/R/allPackage.R
mmnet/R/checkMgrastMetagenome.R
mmnet/R/constructMetabolicNetwork.R
mmnet/R/constuctSSN.R
mmnet/R/delMgrastInbox.R
mmnet/R/differentialAnalyzeNet.R
mmnet/R/estimateAbundance.R
mmnet/R/generateMgrastWebkey.R
mmnet/R/generateMgrastWebsession.R
mmnet/R/getKOPathwayInfo.R
mmnet/R/getMgrastAnnotation.R
mmnet/R/listMgrastInbox.R
mmnet/R/listMgrastProject.R
mmnet/R/loadMetabolicData.R
mmnet/R/loginMgrast.R
mmnet/R/preprocessKOMetabolites.R
mmnet/R/saveMetabolicData.R
mmnet/R/showMetagenomicNet.R
mmnet/R/submitMgrastJob.R
mmnet/R/topologicalAnalyzeNet.R
mmnet/R/updateKEGGPathway.R
mmnet/R/uploadMgrast.R
mmnet/R/validity-methods.R
mmnet/build
mmnet/build/vignette.rds
mmnet/data
mmnet/data/RefDbcache.rda
mmnet/data/anno.rda
mmnet/data/datalist
mmnet/inst
mmnet/inst/doc
mmnet/inst/doc/mmnet.R
mmnet/inst/doc/mmnet.Rnw
mmnet/inst/doc/mmnet.pdf
mmnet/inst/extdata
mmnet/inst/extdata/IMGSample.tab
mmnet/man
mmnet/man/RefDbcache.Rd
mmnet/man/anno.Rd
mmnet/man/checkMgrastMetagenome.Rd
mmnet/man/constructMetabolicNetwork.Rd
mmnet/man/constructSSN.Rd
mmnet/man/delMgrastInbox.Rd
mmnet/man/differentialAnalyzeNet.Rd
mmnet/man/estimateAbundance.Rd
mmnet/man/generateMgrastWebkey.Rd
mmnet/man/generateMgrastWebsession.Rd
mmnet/man/getKOPathwayInfo.Rd
mmnet/man/getMgrastAnnotation.Rd
mmnet/man/listMgrastInbox.Rd
mmnet/man/listMgrastProject.Rd
mmnet/man/loadMetabolicData.Rd
mmnet/man/loginMgrast.Rd
mmnet/man/mmnet-package.Rd
mmnet/man/preprocessKOMetabolites.Rd
mmnet/man/saveMetabolicData.Rd
mmnet/man/showMetagenomicNet.Rd
mmnet/man/submitMgrastJob.Rd
mmnet/man/topologicalAnalyzeNet.Rd
mmnet/man/updateKEGGPathway.Rd
mmnet/man/uploadMgrast.Rd
mmnet/vignettes
mmnet/vignettes/Refnet.png
mmnet/vignettes/mmnet.Rnw
mmnet/vignettes/mmnet.bib