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: 1.26.0 Date: 2022-10-28 Maintainer: Benjamin Callahan Author: Benjamin Callahan , 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 git_url: https://git.bioconductor.org/packages/dada2 git_branch: RELEASE_3_16 git_last_commit: 71af423 git_last_commit_date: 2022-11-01 Date/Publication: 2022-11-01 NeedsCompilation: yes Packaged: 2022-11-01 21:19:11 UTC; biocbuild Built: R 4.2.3; x86_64-pc-linux-gnu; 2023-04-27 03:24:23 UTC; unix