Package: decontam 1.27.0

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]

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decontam.pdf |decontam.html✨
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-1.27.0(bioc 3.21)decontam-1.26.0(bioc 3.20)

immunooncologymicrobiomesequencingclassificationmetagenomicsampliconbioinformaticscontaminationmetabarcoding

11.36 score 153 stars 5 packages 524 scripts 2.4k downloads 76 mentions 4 exports 33 dependencies

Last updated 4 months agofrom:2222effe26. Checks:3 OK, 5 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 15 2025
R-4.5-winNOTEFeb 15 2025
R-4.5-macNOTEFeb 15 2025
R-4.5-linuxNOTEFeb 15 2025
R-4.4-winNOTEFeb 15 2025
R-4.4-macNOTEFeb 15 2025
R-4.3-winOKFeb 15 2025
R-4.3-macOKFeb 15 2025

Exports:isContaminantisNotContaminantplot_conditionplot_frequency

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbleutf8vctrsviridisLitewithr

Introduction to decontam

Benjamin Callahan, Nicole Davis

Rendered fromdecontam_intro.Rmdusingknitr::rmarkdownon Feb 15 2025.

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