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 genus-species

assignment by exact matching.

Version: 1.8.0

Date: 2018-1-30

Maintainer: Benjamin Callahan <[email protected]>

Author: Benjamin Callahan <[email protected]>, 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