This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

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 (3.18)

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 [aut, cre], Nicole Marie Davis [aut], Felix G.M. Ernst [ctb]

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

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("decontam")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("decontam")
Introduction to dada2 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software
Version 1.21.0
In Bioconductor since BioC 3.7 (R-3.5) (5.5 years)
License Artistic-2.0
Depends R (>= 3.4.1), methods (>= 3.4.1)
Imports ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats
Linking To
Suggests BiocStyle, knitr, rmarkdown, phyloseq
System Requirements
Enhances
URL https://github.com/benjjneb/decontam
Bug Reports https://github.com/benjjneb/decontam/issues
See More
Depends On Me
Imports Me mia
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package decontam_1.21.0.tar.gz
Windows Binary decontam_1.21.0.zip (64-bit only)
macOS Binary (x86_64) decontam_1.21.0.tgz
macOS Binary (arm64) decontam_1.21.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/decontam
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/decontam
Bioc Package Browser https://code.bioconductor.org/browse/decontam/
Package Short Url https://bioconductor.org/packages/decontam/
Package Downloads Report Download Stats