decontam
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
Bioconductor version: 3.23 · Package version: 1.32.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("decontam")Details
| Maintainer | Benjamin Callahan <benjamin.j.callahan@gmail.com> |
| Author | Benjamin Callahan [aut, cre], Nicole Marie Davis [aut], Felix G.M. Ernst [ctb] (ORCID: <https://orcid.org/0000-0001-5064-0928>) |
| License | Artistic-2.0 |
| URL | https://github.com/benjjneb/decontam |
| Bug Reports | https://github.com/benjjneb/decontam/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/decontam/ |
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 1.32.0, https://bioconductor.org/packages/decontam.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | decontam_1.32.0.tar.gz |
| Windows binary (x86_64) | decontam_1.32.0.zip |
| macOS binary (arm64) | decontam_1.32.0.tgz |
| macOS binary (x86_64) | decontam_1.32.0.tgz |
Dependencies
Depends: R (>= 3.4.1), methods (>= 3.4.1)
Imports: ggplot2 (>= 2.1.0), reshape2 (>= 1.4.1), stats
Reverse dependencies
Imports Me (1): mia