dada2
Accurate, high-resolution sample inference from amplicon sequencing data
Bioconductor version: Release (3.19)
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.
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 "4.4") 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 | |
| LICENSE | Text |
Details
| biocViews | Classification, ImmunoOncology, Metagenomics, Microbiome, Sequencing, Software |
| Version | 1.32.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 years) |
| License | LGPL-2 |
| 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) |
| 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 | MiscMetabar |
| Imports Me | Rbec, DBTC |
| Suggests Me | mia |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | dada2_1.32.0.tar.gz |
| Windows Binary (x86_64) | dada2_1.32.0.zip (64-bit only) |
| macOS Binary (x86_64) | dada2_1.32.0.tgz |
| macOS Binary (arm64) | dada2_1.32.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/dada2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/dada2 |
| Bioc Package Browser | https://code.bioconductor.org/browse/dada2/ |
| Package Short Url | https://bioconductor.org/packages/dada2/ |
| Package Downloads Report | Download Stats |