Rbec

DOI: 10.18129/B9.bioc.Rbec    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see Rbec.

Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities

Bioconductor version: 3.13

Rbec is a adapted version of DADA2 for analyzing amplicon sequencing data from synthetic communities (SynComs), where the reference sequences for each strain exists. Rbec can not only accurately profile the microbial compositions in SynComs, but also predict the contaminants in SynCom samples.

Author: Pengfan Zhang [aut, cre]

Maintainer: Pengfan Zhang <pzhang at mpipz.mpg.de>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Rbec")

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("Rbec")

 

HTML	R Script	Rbec
PDF		Reference Manual

Details

biocViews	MicrobialStrain, Microbiome, Sequencing, Software
Version	1.0.0
In Bioconductor since	BioC 3.13 (R-4.1) (< 6 months)
License	LGPL-3
Depends
Imports	Rcpp (>= 1.0.6), dada2, ggplot2, readr, doParallel, foreach, grDevices, stats, utils
LinkingTo	Rcpp
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	Rbec_1.0.0.tar.gz
Windows Binary	Rbec_1.0.0.zip
macOS 10.13 (High Sierra)	Rbec_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Rbec
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Rbec
Package Short Url	https://bioconductor.org/packages/Rbec/
Package Downloads Report	Download Stats