mmnet: A metagenomic pipeline for systems biology
Version 1.13.0

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.

AuthorYang Cao, Fei Li
Bioconductor views GraphsAndNetwork Microbiome Pathways Sequencing SystemsBiology
Date of publicationNone
MaintainerYang Cao <yiluheihei@gmail.com>, Fei Li <pittacus@gmail.com>
LicenseGPL (>= 2)
Version1.13.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("mmnet")

Getting started

Package overview

Popular man pages

anno: annotation profile of two sample data sets
differentialAnalyzeNet: the KO difference abundance of specific state
estimateAbundance: Getting KO (KEGG ontology) and abundance information
getKOPathwayInfo: Get the KEGG metabolic pathway information
loginMgrast: Login to the MGRAST
mmnet-package: A metagenomic pipeline for systems biology
updateKEGGPathway: Updating and saving the reference (KEGG metabolic pathway)...
See all...

All man pages Function index File listing

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

Functions

RefDbcache Man page
anno Man page
checkMgrastMetagenome Man page Source code
constructMetabolicNetwork Man page Source code
constructSSN Man page Source code
delMgrastInbox Man page Source code
differentialAnalyzeNet Source code
differentialAnalyzeNet Man page
estimateAbundance Man page Source code
extract_metadata Source code
generateMgrastWebkey Man page Source code
generateMgrastWebsession Man page Source code
getKOPathwayInfo Man page Source code
getMgrastAnnotation Man page Source code
listMgrastInbox Man page Source code
listMgrastProject Man page Source code
loadMetabolicData Man page Source code
loginMgrast Man page Source code
make_biom Source code
mmnet-package Man page
preprocessKOMetabolites Man page Source code
read_biom Source code
saveMetabolicData Man page Source code
showMetagenomicNet Man page Source code
submitMgrastJob Man page Source code
topologicalAnalyzeNet Man page Source code
updateKEGGPathway Man page Source code
uploadMgrast Man page Source code
validbiom Source code
write_biom Source code

Files

.BBSoptions
DESCRIPTION
NAMESPACE
R
R/BIOM-class.R
R/IO-methods.R
R/allClasses.R
R/allPackage.R
R/checkMgrastMetagenome.R
R/constructMetabolicNetwork.R
R/constuctSSN.R
R/delMgrastInbox.R
R/differentialAnalyzeNet.R
R/estimateAbundance.R
R/generateMgrastWebkey.R
R/generateMgrastWebsession.R
R/getKOPathwayInfo.R
R/getMgrastAnnotation.R
R/listMgrastInbox.R
R/listMgrastProject.R
R/loadMetabolicData.R
R/loginMgrast.R
R/preprocessKOMetabolites.R
R/saveMetabolicData.R
R/showMetagenomicNet.R
R/submitMgrastJob.R
R/topologicalAnalyzeNet.R
R/updateKEGGPathway.R
R/uploadMgrast.R
R/validity-methods.R
build
build/vignette.rds
data
data/RefDbcache.rda
data/anno.rda
data/datalist
inst
inst/doc
inst/doc/mmnet.R
inst/doc/mmnet.Rnw
inst/doc/mmnet.pdf
inst/extdata
inst/extdata/IMGSample.tab
man
man/RefDbcache.Rd
man/anno.Rd
man/checkMgrastMetagenome.Rd
man/constructMetabolicNetwork.Rd
man/constructSSN.Rd
man/delMgrastInbox.Rd
man/differentialAnalyzeNet.Rd
man/estimateAbundance.Rd
man/generateMgrastWebkey.Rd
man/generateMgrastWebsession.Rd
man/getKOPathwayInfo.Rd
man/getMgrastAnnotation.Rd
man/listMgrastInbox.Rd
man/listMgrastProject.Rd
man/loadMetabolicData.Rd
man/loginMgrast.Rd
man/mmnet-package.Rd
man/preprocessKOMetabolites.Rd
man/saveMetabolicData.Rd
man/showMetagenomicNet.Rd
man/submitMgrastJob.Rd
man/topologicalAnalyzeNet.Rd
man/updateKEGGPathway.Rd
man/uploadMgrast.Rd
vignettes
vignettes/Refnet.png
vignettes/mmnet.Rnw
vignettes/mmnet.bib
mmnet documentation built on May 20, 2017, 10:50 p.m.

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