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: 1.10.0
Date: 2018-10-10
Maintainer: Benjamin Callahan <benjamin.j.callahan@gmail.com>
Author: Benjamin Callahan <benjamin.j.callahan@gmail.com>, Paul McMurdie, Susan Holmes
License: LGPL-3
LazyLoad: yes
Depends: R (>= 3.2.0), Rcpp (>= 0.11.2), methods (>= 3.2.0)
Imports: Biostrings (>= 2.42.1), ggplot2 (>= 2.1.0), data.table (>=
        1.9.4), 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: 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: 6.0.1
git_url: https://git.bioconductor.org/packages/dada2
git_branch: RELEASE_3_8
git_last_commit: 0d06ef2
git_last_commit_date: 2018-10-30
Date/Publication: 2018-10-30
NeedsCompilation: yes
Packaged: 2018-10-31 01:08:39 UTC; biocbuild
Built: R 3.5.1; x86_64-conda_cos6-linux-gnu; 2018-12-19 17:04:09 UTC; unix
