dada2
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see dada2.
Accurate, high-resolution sample inference from amplicon sequencing data
Bioconductor version: 3.7
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.
Author: Benjamin Callahan <benjamin.j.callahan at gmail.com>, Paul McMurdie, Susan Holmes
Maintainer: Benjamin Callahan <benjamin.j.callahan at gmail.com>
citation("dada2")
):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("dada2")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("dada2")
Introduction to dada2 | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Classification, Metagenomics, Microbiome, Sequencing, Software |
Version | 1.8.0 |
In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
License | LGPL-3 |
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) |
System Requirements | GNU make |
URL | http://benjjneb.github.io/dada2/ |
Bug Reports | https://github.com/benjjneb/dada2/issues |
See More
Suggests | BiocStyle, knitr, rmarkdown |
Linking To | Rcpp, RcppParallel |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | dada2_1.8.0.tar.gz |
Windows Binary | dada2_1.8.0.zip (32- & 64-bit) |
Mac OS X 10.11 (El Capitan) | dada2_1.8.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/dada2 |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/dada2 |
Package Short Url | https://bioconductor.org/packages/dada2/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.7 | Source Archive |