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.
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 command-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/decontam", repos = NULL, type = "source",
dependencies = c("Depends", "Suggests","Imports"))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