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
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Accurate, high-resolution sample inference from amplicon sequencing data
Bioconductor version: Release (3.4)
The dada2 package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. The dada2 pipeline inputs 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.
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 | 1.2.2 |
| In Bioconductor since | BioC 3.3 (R-3.3) (1 year) |
| License | LGPL-3 |
| Depends | R (>= 3.2.0), Rcpp (>= 0.11.2), methods (>= 3.2.0) |
| Imports | Biostrings(>= 2.32.1), ggplot2 (>= 1.0), data.table (>= 1.9.4), reshape2 (>= 1.4.1), ShortRead(>= 1.24.0), RcppParallel (>= 4.3.0), parallel (>= 3.2.0) |
| LinkingTo | Rcpp, RcppParallel |
| Suggests | testthat (>= 0.9.1), BiocStyle, knitr, rmarkdown |
| SystemRequirements | GNU make |
| 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_1.2.2.tar.gz |
| Windows Binary | dada2_1.2.2.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | dada2_1.2.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/dada2/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/dada2/ |
| Package Downloads Report | Download Stats |
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