Identifying contaminants in marker-gene and metagenomics data | Introduction | Necessary Ingredients | Setting up | Inspect Library Sizes | Identify Contaminants - Frequency | Identify Contaminants - Prevalence | Putting It All Together | Conclusion
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:
decontam_1.33.0.tar.gz
decontam_1.33.0.zip(r-4.7)decontam_1.33.0.zip(r-4.6)decontam_1.33.0.zip(r-4.5)
decontam_1.33.0.tgz(r-4.6-any)decontam_1.33.0.tgz(r-4.5-any)
decontam_1.33.0.tar.gz(r-4.7-any)decontam_1.33.0.tar.gz(r-4.6-any)
decontam_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
decontam/json (API)
| # 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
Last updated from:afdb4e8505. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 171 | ||
| linux-devel-x86_64 | NOTE | 157 | ||
| source / vignettes | OK | 206 | ||
| linux-release-x86_64 | NOTE | 206 | ||
| macos-release-arm64 | NOTE | 146 | ||
| macos-oldrel-arm64 | NOTE | 88 | ||
| windows-devel | NOTE | 88 | ||
| windows-release | NOTE | 93 | ||
| windows-oldrel | NOTE | 107 | ||
| wasm-release | OK | 154 |
Exports:isContaminantisNotContaminantplot_conditionplot_frequency
Dependencies:clicpp11farverggplot2gluegtableisobandlabelinglifecyclemagrittrplyrR6RColorBrewerRcppreshape2rlangS7scalesstringistringrvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Identify contaminant sequences. | isContaminant isContaminant,ANY-method |
| Identify non-contaminant sequences. | isNotContaminant isNotContaminant,ANY-method |
| Plot DNA concentrations as a function of experimental conditions. | plot_condition |
| Plot frequencies as a function of input DNA concentration | plot_frequency |
