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MelonnPan Tutorial

MelonnPan (Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles) is a computational method for predicting metabolite compositions from shotgun metagenomic sequencing data.

MelonnPan can be installed using our quickstart documentation. For additional information, please refer to the MelonnPan paper (Himel Mallick, Eric A. Franzosa, Lauren J. McIver, Soumya Banerjee, Alexandra Sirota-Madi, Aleksandar D. Kostic, Clary B. Clish, Hera Vlamakis, Ramnik Xavier, Curtis Huttenhower (2017+). "Predictive metabolomic profiling of microbial communities using shotgun metagenomic sequences" (In progress)).

Support is available from the MelonnPan Google Group. Feel free to join the group or to post any questions directly by emailing melonnpan-user@googlegroups.com.



Overview

MelonnPan.png

1. Setup

1.1 Requirements

  • R software ( version >= 3.3.2)
  • Plus the following R packages: glmnet, HDtweedie, getopt, doParallel, vegan, GenABEL, and data.table

1.2 Installation

Install MelonnPan by first obtaining the source code. Then install the dependencies and install the software. Run the following commands to install MelonnPan and its dependencies.

$ git clone https://github.com/biobakery/melonnpan.git
$ R -q -e "install.packages(c('glmnet','HDtweedie','getopt','doParallel','vegan','GenABEL','data.table'), repos='http://cran.r-project.org')"
$ R CMD INSTALL melonnpan

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