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mmnet (version 1.10.2)

A metagenomic pipeline for systems biology

Description

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.

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Version

Version

1.10.2

License

GPL (>= 2)

Maintainer

Yang Cao

Last Published

February 15th, 2017

Functions in mmnet (1.10.2)

anno

annotation profile of two sample data sets
constructSSN

construct the state specific network
generateMgrastWebsession

Generate your websession
preprocessKOMetabolites

Preprocessing of KO's (enzyme's) metabolites
mmnet-package

A metagenomic pipeline for systems biology
loginMgrast

Login to the MGRAST
showMetagenomicNet

Visualiation of metabolic network
loadMetabolicData

Metabolic data loading
submitMgrastJob

Create a job on MGRAST
topologicalAnalyzeNet

Analyze the specific state network
estimateAbundance

Getting KO (KEGG ontology) and abundance information
differentialAnalyzeNet

the KO difference abundance of specific state
getMgrastAnnotation

Get the annotation profile from MGRAST
checkMgrastMetagenome

Check whether the MGRAST annotation is completed
RefDbcache

Reference data for global metabolic construction
updateKEGGPathway

Updating and saving the reference (KEGG metabolic pathway) data
listMgrastProject

List all the private projects you summitted to MGRAST
constructMetabolicNetwork

Metabolic network construction of microbiome
listMgrastInbox

List the contents of the user inbox
saveMetabolicData

Save a new version of the reference metabolic data
getKOPathwayInfo

Get the KEGG metabolic pathway information
generateMgrastWebkey

Generate your webkey on MGRAST
uploadMgrast

Upload your sequence to MGRAST
delMgrastInbox

Delete the files in you MG-RAST inbox