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Rbec

This is the development version of Rbec; for the stable release version, see Rbec.

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


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews MicrobialStrain, Microbiome, Sequencing, Software
Version 1.11.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License LGPL-3
Depends
Imports Rcpp (>= 1.0.6), dada2, ggplot2, readr, doParallel, foreach, grDevices, stats, utils
System Requirements
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Suggests knitr, rmarkdown
Linking To Rcpp
Enhances
Depends On Me
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Links To Me
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Package Archives

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

Source Package Rbec_1.11.0.tar.gz
Windows Binary Rbec_1.11.0.zip
macOS Binary (x86_64) Rbec_1.11.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/Rbec
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/Rbec
Bioc Package Browser https://code.bioconductor.org/browse/Rbec/
Package Short Url https://bioconductor.org/packages/Rbec/
Package Downloads Report Download Stats