decontam
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see decontam.
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
Bioconductor version: 3.9
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("decontam")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Classification, ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 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 |
See More
| Suggests | BiocStyle, knitr, rmarkdown, phyloseq |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | decontam_1.4.0.tar.gz |
| Windows Binary | decontam_1.4.0.zip |
| Mac OS X 10.11 (El Capitan) | decontam_1.4.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |