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