Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
Switch branches/tags
Nothing to show
Clone or download
bcallah bcallah
bcallah and bcallah Stubbed in plot_condition
This function plots DNA concentration against conditions of interest,
to visually check for potential associations that could interact w/ the
decontam frequency method.
Latest commit 5c1b9cb Jun 1, 2018

README.md

Documentation

An introductory vignette demonstrating how to use the decontam package to identify contaminants.

The preprint introducing decontam with benchmarking demonstrating how decontam-inating your data removes reagent sequences, improves accuracy, reduces batch effects, and prevents false-positive assocations.

More documentation available through the R help interface (e.g. ?isContaminant) and at the decontam web site.

Installation

The decontam R package is currently available as a source package through github, so installation requires the ability to compile R packages. This means that R and the R tool-chain must be installed, which requires the Xcode comnand-line tools on Mac and Rtools on Windows.

The easiest installation method uses the devtools package:

library(devtools)
devtools::install_github("benjjneb/decontam")

Alternatively you can install from source by hand. First download the zipped package and unzip it (or expand the tarball). Start a fresh R session, and enter the following.

install.packages("path/to/dada2", repos = NULL, type = "source",
                 dependencies = c("Depends", "Suggests","Imports"))

Other Resources

Bugs and difficulties in using decontam are welcome on the issue tracker.

Planned feature improvements are also publicly catalogued at on the "Issues" page for decontam: https://github.com/benjjneb/decontam/issues