DESCRIPTION

Package: dada2
Type: Package
Title: Accurate, high-resolution sample inference from amplicon sequencing data
Description: The dada2 package 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.
Version: 1.35.4
Date: 2023-04-09
Maintainer: Benjamin Callahan <benjamin.j.callahan@gmail.com>
Author: Benjamin Callahan <benjamin.j.callahan@gmail.com>, Paul McMurdie, Susan Holmes
License: LGPL-2
LazyLoad: yes
Depends:
    R (>= 3.4.0),
    Rcpp (>= 0.12.0),
    methods (>= 3.4.0)
Imports:
    Biostrings (>= 2.42.1),
    ggplot2 (>= 2.1.0),
    reshape2 (>= 1.4.1),
    ShortRead (>= 1.32.0),
    RcppParallel (>= 4.3.0),
    parallel (>= 3.2.0),
    IRanges (>= 2.6.0),
    XVector (>= 0.16.0),
    BiocGenerics (>= 0.22.0)
Suggests:
    BiocStyle,
    knitr,
    rmarkdown
LinkingTo:
    Rcpp,
    RcppParallel
SystemRequirements: GNU make
VignetteBuilder: knitr
biocViews: ImmunoOncology, Microbiome, Sequencing, Classification, Metagenomics
URL: http://benjjneb.github.io/dada2/
BugReports: https://github.com/benjjneb/dada2/issues
LazyData: true
Collate:
    'RcppExports.R'
    'allClasses.R'
    'allPackage.R'
    'chimeras.R'
    'dada.R'
    'errorModels.R'
    'filter.R'
    'misc.R'
    'multiSample.R'
    'paired.R'
    'plot-methods.R'
    'sequenceIO.R'
    'show-methods.R'
    'taxonomy.R'
RoxygenNote: 7.1.1