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Package: r-bioc-dada2 (1.14.1+dfsg-1)

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: libc6 (>= 2.29)
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
  • dep: libgcc-s1 (>= 3.0)
    GCC support library
  • dep: libstdc++6 (>= 5.2)
    GNU Standard C++ Library v3
  • dep: libtbb2 (>= 2017~U7)
    parallelism library for C++ - runtime files
  • dep: r-api-3.5
    virtual package provided by r-base-core
  • dep: r-api-bioc-3.10
    virtual package provided by r-bioc-biocgenerics
  • dep: r-base-core (>=
    GNU R core of statistical computation and graphics system
  • dep: r-bioc-biocgenerics (>= 0.22.0)
    generic functions for Bioconductor
  • dep: r-bioc-biostrings (>= 2.42.1)
    GNU R string objects representing biological sequences
  • 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)
    BioConductor representation and manpulation of external sequences
  • dep: r-cran-ggplot2 (>= 2.1.0)
    implementation of the Grammar of Graphics
  • dep: r-cran-rcpp (>= 0.12.0)
    GNU R package for Seamless R and C++ Integration
  • dep: r-cran-rcppparallel (>= 4.3.0)
    parallel programming tools for Rcpp
  • dep: r-cran-reshape2 (>= 1.4.1)
    Flexibly reshape data: a reboot of the reshape package
  • sug: libjs-jquery
    JavaScript library for dynamic web applications
  • sug: r-cran-knitr
    GNU R package for dynamic report generation using Literate Programming
  • sug: r-cran-rmarkdown
    convert R markdown documents into a variety of formats

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