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decontam

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

Identify Contaminants in Marker-gene and Metagenomics Sequencing Data

DOI: 10.18129/B9.bioc.decontam

Bioconductor version: Development (3.24)

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: 0000-0001-5064-0928

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

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

Benjamin Callahan, Nicole Marie Davis. decontam: Identify Contaminants in Marker-gene and Metagenomics Sequencing Data. doi:10.18129/B9.bioc.decontam, R package version 1.33.0, https://bioconductor.org/packages/decontam.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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")

Details

Package Archives

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