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.

AuthorYang Cao, Fei Li
Date of publicationNone
MaintainerYang Cao <yiluheihei@gmail.com>, Fei Li <pittacus@gmail.com>
LicenseGPL (>= 2)
Version1.12.0

View on Bioconductor

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

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