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:
decontam_1.27.0.tar.gz
decontam_1.27.0.zip(r-4.5)decontam_1.27.0.zip(r-4.4)decontam_1.27.0.zip(r-4.3)
decontam_1.27.0.tgz(r-4.4-any)decontam_1.27.0.tgz(r-4.3-any)
decontam_1.27.0.tar.gz(r-4.5-noble)decontam_1.27.0.tar.gz(r-4.4-noble)
decontam_1.27.0.tgz(r-4.4-emscripten)decontam_1.27.0.tgz(r-4.3-emscripten)
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
Last updated 2 months agofrom:2222effe26. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 17 2024 |
| R-4.5-win | NOTE | Dec 17 2024 |
| R-4.5-linux | NOTE | Dec 17 2024 |
| R-4.4-win | NOTE | Dec 17 2024 |
| R-4.4-mac | NOTE | Dec 17 2024 |
| R-4.3-win | OK | Dec 17 2024 |
| R-4.3-mac | OK | Dec 17 2024 |
Exports:isContaminantisNotContaminantplot_conditionplot_frequency
Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbleutf8vctrsviridisLitewithr
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 |
