decontam

DOI: 10.18129/B9.bioc.decontam    

This is the development version of decontam; for the stable release version, see decontam.

Identify Contaminants in Marker-gene and Metagenomics Sequencing Data

Bioconductor version: Development (3.8)

Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs,...). Requires DNA quantitation data or sequenced negative control samples.

Author: Benjamin Callahan <benjamin.j.callahan at gmail.com>, Nicole Marie Davis

Maintainer: Benjamin Callahan <benjamin.j.callahan at gmail.com>

Citation (from within R, enter citation("decontam")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("decontam")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("decontam")

 

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PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, Metagenomics, Microbiome, Sequencing, Software
Version 1.1.0
License Artistic-2.0
Depends R (>= 3.4.1), methods (>= 3.4.1)
Imports ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, phyloseq
SystemRequirements
Enhances
URL https://github.com/benjjneb/decontam
BugReports https://github.com/benjjneb/decontam/issues
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package decontam_1.1.0.tar.gz
Windows Binary decontam_1.1.0.zip
Mac OS X 10.11 (El Capitan) decontam_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/decontam
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/decontam
Package Short Url http://bioconductor.org/packages/decontam/
Package Downloads Report Download Stats

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