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Пакет: r-bioc-dada2 (1.22.0+dfsg-1build2)

sample inference from amplicon sequencing data

The dada2 package contributes to software workflows to interpret sequencing data from microbiota - the relative abundance of bacterial and/or yeast, typically measured in the gut. It infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.

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  • dep: libstdc++6 (>= 11)
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  • dep: r-base-core (>= 4.1.2-1ubuntu2)
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  • dep: r-bioc-biostrings (>= 2.42.1)
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  • dep: r-bioc-iranges (>= 2.6.0)
    GNU R low-level containers for storing sets of integer ranges
  • dep: r-bioc-shortread (>= 1.32.0)
    GNU R classes and methods for high-throughput short-read sequencing data
  • dep: r-bioc-xvector (>= 0.16.0)
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  • dep: r-cran-ggplot2 (>= 2.1.0)
    implementation of the Grammar of Graphics
  • dep: r-cran-rcpp (>= 0.12.0)
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  • dep: r-cran-rcppparallel (>= 4.3.0)
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  • dep: r-cran-reshape2 (>= 1.4.1)
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  • sug: r-bioc-biocstyle
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