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

Functions

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

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.