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{"name":"mmgenome","tagline":"Tools for extracting individual genomes from metagneomes","body":"### What is mmgenome?\r\nThe mmgenome toolbox enables reproducible extraction of individual genomes from metagenomes. It builds on the [multi-metagenome](http://madsalbertsen.github.io/multi-metagenome/) concept, but wraps most of the process of extracting genomes in simple R functions. Thereby making the whole process of binning easy and at the same time reproducible through the Rmarkdown format. \r\n\r\nThe mmgenome R package also facilitates effortless integration with additional data sources and hence should not be seen as \"yet another binning method\", but rather a package to integrate different binning strategies. \r\n\r\nThe package is currently in beta stage and we'll be updating the documentation here shortly. All functions in the mmgenome R package has associated documentation, check it out in R by e.g. `?mmplot`.\r\n\r\n### How does it work?\r\nCheck out our examples of [loading data](http://madsalbertsen.github.io/mmgenome/Load_data.html) and [extracting genomes](http://madsalbertsen.github.io/mmgenome/Genome_extraction.html) in the mmgenome R package. The associated Rmarkdown files can be found in the folder mmgenome/workflows.\r\n\r\n### Getting started\r\nInstall the latest version of [R (>3.1)](http://www.r-project.org/), [Rtools](http://www.r-project.org/) and [RStudio](http://www.rstudio.com/). Then go ahead and install the mmgenome R package directly from github using the devtools package.\r\n\r\n```\r\ninstall.packages(\"devtools\")\r\ndevtools::install_github(\"MadsAlbertsen/mmgenome/mmgenome\")\r\n```\r\n\r\nYou might need to install `Biostrings` through `bioconductor` depending on your version of R. However, it's quite easily done.\r\n```\r\nsource(\"http://bioconductor.org/biocLite.R\")\r\nbiocLite(\"Biostrings\")\r\n```\r\n\r\nTo generate your own data simply clone repository and setup the shell script mmgenome/workflows/data.generation.2.1.0.sh.\r\n```\r\ngit clone https://github.com/MadsAlbertsen/mmgenome.git\r\n```","google":"UA-53930589-1","note":"Don't delete this file! It's used internally to help with page regeneration."}