- Course overview
- Search within this course
- Introduction
- Course materials and software
- Metagenomics bioinformatics – course introduction
- Quality control and host decontamination
- The European Nucleotide Archive
- Tools to assemble short reads
- MGnify services
- MGnifyR
- Binning and MAG generation
- ENA metagenomics standards
- MGnify MAG resources
- Strain resolution
- Tools for comparative metagenomics
- Your feedback
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
MGnifyR
Ben Allen, from the University of Newcastle, introduces MGnifyR – an R package that allows users to access and analyse MGnify data using the R programming language.
This talk walks through the process of carrying out an analysis with MGnifyR including installing the package, generating objects, searching MGnify, and downloading metadata and raw files.
Practical
This practical will introduce you to the basics of MGnifyR and help you gain an idea of how it can be used to explore microbiome data. You don’t need to be an expert R coder to follow the practical, but you might want to work through the R Data Frame tutorial before you begin.
All the necessary information you need for this practical can be found below:
You will need to have R installed on your computer to run the practical, but the step by step instructions will guide you through installing the latest MGnifyR package. Please note that the package is still in development and bugs are routinely corrected.