Metagenomics Analysis Tools: the matR package

The matR package and manual (HTML; pdf) are available on CRAN; see Installation at the bottom of this page to get started. Just below, some extended tutorials are available in HTML and pdf versions. Also, with matR loaded you can execute these in your R session, for example with:

step.through(file="http://mg-rast.github.io/matR/analysis-in-a-nutshell.R")

In the same way Other scripts listed below can be viewed here or executed locally. The Extensions section lists add-ons to the CRAN version of the package. There’s no reason to step through them line by line, but the extra functionality they provide can be introduced to your R session, for example with:

source(file="http://mg-rast.github.io/matR/local-workbench.R")

Please credit this software if it assists your work. R proposes a standard form for package citation shown by:

citation("matR")

Check out our Google group (matR-forum) for discussion and help.

Tutorials

• HTML | pdf | source : analysis-in-a-nutshell

• HTML | pdf | source : six-analyses-for-any-metagenome

• HTML | pdf | source : annotation-distribution
• HTML | pdf | source : creating-heatmaps
• HTML | pdf | source : plotting-principal-components

• HTML | pdf | source : about-analysis-functions

• HTML | pdf | source : retrieving-annotations
• HTML | pdf | source : handling-biom

• HTML | pdf | source : normalizing-data

• HTML | pdf | source : help

Extensions

• source : local-workbench.R
• source : six-simple-analyses.R

Other scripts

• none right now

Installation

Make sure to have a current version of the R language. Then open an R session and install with:

install.packages('matR', dependencies=TRUE)
library(matR)
dependencies()

Go through the several prompts following dependencies(). Once installed, the package must be loaded during every session with: library(matR).

Old version

Users of the early release version can reinstall it with:

remove.packages('matR')        # if necessary
install.packages('devtools')
library(devtools)
install_github(repo='MG-RAST/matR', ref="early-release")
library(matR)
dependencies()