Package: decontam 1.33.0

Benjamin Callahan

decontam: Identify Contaminants in Marker-gene and Metagenomics Sequencing Data

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.

Authors:Benjamin Callahan [aut, cre], Nicole Marie Davis [aut], Felix G.M. Ernst [ctb]

decontam_1.33.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
decontam/json (API)
NEWS

# Install 'decontam' in R:
install.packages('decontam', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

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

On BioConductor:decontam-1.33.0(bioc 3.24)decontam-1.32.0(bioc 3.23)

immunooncologymicrobiomesequencingclassificationmetagenomicsampliconbioinformaticscontaminationmetabarcoding

11.89 score 170 stars 9 packages 700 scripts 2.7k downloads 76 mentions 4 exports 23 dependencies

Last updated from:afdb4e8505. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING156
linux-devel-x86_64NOTE172
source / vignettesOK220
linux-release-x86_64NOTE223
macos-release-arm64NOTE118
macos-oldrel-arm64NOTE95
windows-develNOTE123
windows-releaseNOTE143
windows-oldrelNOTE89
wasm-releaseOK142

Exports:isContaminantisNotContaminantplot_conditionplot_frequency

Dependencies:clicpp11farverggplot2gluegtableisobandlabelinglifecyclemagrittrplyrR6RColorBrewerRcppreshape2rlangS7scalesstringistringrvctrsviridisLitewithr

Introduction to decontam

Benjamin Callahan, Nicole Davis

Rendered fromdecontam_intro.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2020-07-06
Started: 2017-07-28