mmnet-package: A metagenomic pipeline for systems biology
In mmnet: A metagenomic pipeline for systems biology
Description
The mmnet add-on is an implementation of mapping metagenomic data to the KEGG global metabolic pathway and constructing a systems-level network.
It is of great help to analysis the various functional properties, including regulation and metabolic functionality of the metagenome.
Details
This package contains functions for mapping metagenomic data to the KEGG global metabolic pathway and constructing systems-level network. First, the information of enzymes, corresponding substrates and products is parsed from the KEGG PATYWAY database with function updateKEGGPathway. Second, sequence functional ontology annotation with KEGG is preprocessing on MGRAST, KO abundance can be obtained by parse the MGRAST ontology annotation files with function estimateAbundance. Finally, global metabolic pathway and systems-level network are made to analyze the metabolic functionality of metagenome with function constructMetabolicNetwork, visualization with function showMetagenomicNet
mmnet documentation built on May 31, 2017, 3:25 p.m.
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Description
The mmnet add-on is an implementation of mapping metagenomic data to the KEGG global metabolic pathway and constructing a systems-level network. It is of great help to analysis the various functional properties, including regulation and metabolic functionality of the metagenome.
Details
This package contains functions for mapping metagenomic data to the KEGG global metabolic pathway and constructing systems-level network. First, the information of enzymes, corresponding substrates and products is parsed from the KEGG PATYWAY database with function updateKEGGPathway. Second, sequence functional ontology annotation with KEGG is preprocessing on MGRAST, KO abundance can be obtained by parse the MGRAST ontology annotation files with function estimateAbundance. Finally, global metabolic pathway and systems-level network are made to analyze the metabolic functionality of metagenome with function constructMetabolicNetwork, visualization with function showMetagenomicNet
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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