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: 1.39.0
Date: 2024-12-01
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 (>= 4.1.0), 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: 7.3.1
Config/pak/sysreqs: make libbz2-dev libicu-dev libjpeg-dev liblzma-dev
        libpng-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:30:17 UTC
RemoteUrl: https://github.com/bioc/dada2
RemoteRef: HEAD
RemoteSha: 29f93c25edaa7f3f2252b9203ec9ad2a92ead627
NeedsCompilation: yes
Packaged: 2026-01-22 19:41:11 UTC; root
Built: R 4.6.0; x86_64-w64-mingw32; 2026-01-22 19:43:50 UTC; windows
Archs: x64
