decontam

This is the released version of decontam; for the devel version, see decontam.

Identify Contaminants in Marker-gene and Metagenomics Sequencing Data

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DOI: 10.18129/B9.bioc.decontam

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0001-5064-0928

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

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

Installation

To install this package, start R (version "4.5") and enter:


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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software

Version 1.30.0

In Bioconductor since BioC 3.7 (R-3.5) (7.5 years)

License Artistic-2.0

Depends R (>= 3.4.1), methods (>= 3.4.1)

Imports ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats

System Requirements

URL https://github.com/benjjneb/decontam

Bug Reports https://github.com/benjjneb/decontam/issues

Suggests BiocStyle, knitr, rmarkdown, phyloseq

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Package Archives

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

Source Package decontam_1.30.0.tar.gz

Windows Binary (x86_64) decontam_1.29.0.zip

macOS Binary (x86_64) decontam_1.30.0.tgz

macOS Binary (arm64) decontam_1.30.0.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/

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