To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("dada2")
In most cases, you don't need to download the package archive at all.
dada2
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see dada2.
Accurate, high-resolution sample inference from amplicon sequencing data
Bioconductor version: 3.3
The dada2 package provides "OTU picking" functionality, but instead of picking OTUs the DADA2 algorithm exactly infers samples sequences. The dada2 pipeline starts from demultiplexed fastq files, and outputs inferred sample sequences and associated abundances after removing substitution and chimeric errors. Taxonomic classification is also available via a native implementation of the RDP classifier method.
Author: Benjamin Callahan <benjamin.j.callahan at gmail.com>, Paul McMurdie, Susan Holmes
Maintainer: Benjamin Callahan <benjamin.j.callahan at gmail.com>
Citation (from within R,
enter citation("dada2")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("dada2")
Documentation
| HTML | R Script | Introduction to dada2 |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Classification, Metagenomics, Microbiome, Sequencing, Software |
| Version | 1.0.3 |
| In Bioconductor since | BioC 3.3 (R-3.3) (< 6 months) |
| License | LGPL-3 |
| Depends | R (>= 3.2.0), Rcpp (>= 0.11.2) |
| Imports | Biostrings(>= 2.32.1), ggplot2 (>= 1.0), data.table (>= 1.9.4), reshape2 (>= 1.4.1), ShortRead(>= 1.24.0) |
| LinkingTo | Rcpp |
| Suggests | testthat (>= 0.9.1), microbenchmark (>= 1.4.2), BiocStyle, knitr, rmarkdown |
| SystemRequirements | |
| Enhances | |
| URL | http://benjjneb.github.io/dada2/ |
| BugReports | https://github.com/benjjneb/dada2/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | dada2_1.0.3.tar.gz |
| Windows Binary | dada2_1.0.3.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | dada2_1.0.3.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/dada2/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/dada2/ |
| Package Downloads Report | Download Stats |
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