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>
citation("Rbec")):
Installation
To install this package, start R (version "4.1") 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 |
Details
| biocViews | MicrobialStrain, Microbiome, Sequencing, Software |
| Version | 1.0.0 |
| 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 | |
| URL |
See More
| 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_1.0.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/Rbec/ |
| Package Short Url | https://bioconductor.org/packages/Rbec/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.13 | Source Archive |