dada2
This is the development version of dada2; for the stable release version, see dada2.
Accurate, high-resolution sample inference from amplicon sequencing data
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.41.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | LGPL-2 |
| 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) |
| 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 | Rbec, DBTC, MiscMetabar, QsRutils, tidyGenR |
| Suggests Me | mia, demulticoder |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | dada2_1.41.0.tar.gz |
| Windows Binary (x86_64) | dada2_1.41.0.zip |
| macOS Binary (big-sur-x86_64) | dada2_1.41.0.tgz |
| macOS Binary (sonoma-arm64) | dada2_1.41.0.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 |