Rbec

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

Bioconductor version: Release (3.19)

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>

Citation (from within R, enter citation("Rbec")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("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")

Rbec	HTML	R Script
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	MicrobialStrain, Microbiome, Sequencing, Software
Version	1.12.0
In Bioconductor since	BioC 3.13 (R-4.1) (3.5 years)
License	LGPL-3
Depends
Imports	Rcpp (>= 1.0.6), dada2, ggplot2, readr, doParallel, foreach, grDevices, stats, utils
System Requirements
URL

Suggests	knitr, rmarkdown
Linking To	Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	Rbec_1.12.0.tar.gz
Windows Binary (x86_64)	Rbec_1.12.0.zip
macOS Binary (x86_64)	Rbec_1.12.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/Rbec
Source Repository (Developer Access)	git clone [email protected]:packages/Rbec
Bioc Package Browser	https://code.bioconductor.org/browse/Rbec/
Package Short Url	https://bioconductor.org/packages/Rbec/
Package Downloads Report	Download Stats