decontam

DOI: 10.18129/B9.bioc.decontam  

Identify Contaminants in Marker-gene and Metagenomics Sequencing Data

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Introduction to dada2
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software
Version	1.18.0
In Bioconductor since	BioC 3.7 (R-3.5) (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
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	mia
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	decontam_1.18.0.tar.gz
Windows Binary	decontam_1.18.0.zip
macOS Binary (x86_64)	decontam_1.18.0.tgz
macOS Binary (arm64)	decontam_1.18.0.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