A metagenomic pipeline for systems biology


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Documentation for package ‘mmnet’ version 1.8.1

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mmnet-package A metagenomic pipeline for systems biology
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
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) data
uploadMgrast Upload your sequence to MGRAST