hnumcc / decontam

DNA concentration and negative control

Documentation

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

An extensive investigation of contamination in an oral mucosal dataset, that includes evaluation of deontam results.

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

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

Installation

The decontam R package is most easily installed from the Bioconductor repository. To install the most recent version of the decontam package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("decontam")

See the Bioconductor documentation for decontam for additional information.

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

The easiest source installation method uses the devtools package:

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

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