# A metagenomic pipeline for systems biology

## Documentation for package ‘mmnet’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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