RefDbcache              Reference data for global metabolic
                        construction
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
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
