Rbec

DOI: 10.18129/B9.bioc.Rbec    

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

Bioconductor version: Release (3.14)

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 "4.1") 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 1.2.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 years)
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_1.2.0.tar.gz
Windows Binary Rbec_1.2.0.zip
macOS 10.13 (High Sierra) Rbec_1.2.0.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
Old Source Packages for BioC 3.14 Source Archive

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