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✨
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NEWS

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

Peer review:

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

11.33 score 150 stars 5 packages 486 scripts 2.5k downloads 76 mentions 4 exports 33 dependencies

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

TargetResultLatest binary
Doc / VignettesOKJan 16 2025
R-4.5-winNOTEJan 16 2025
R-4.5-linuxNOTEJan 16 2025
R-4.4-winNOTEJan 16 2025
R-4.4-macNOTEJan 16 2025
R-4.3-winOKJan 16 2025
R-4.3-macOKJan 16 2025

Exports:isContaminantisNotContaminantplot_conditionplot_frequency

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbleutf8vctrsviridisLitewithr

Introduction to decontam

Benjamin Callahan, Nicole Davis

Rendered fromdecontam_intro.Rmdusingknitr::rmarkdownon Jan 16 2025.

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