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metabinR

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

Abundance and Compositional Based Binning of Metagenomes


Bioconductor version: Development (3.19)

Provide functions for performing abundance and compositional based binning on metagenomic samples, directly from FASTA or FASTQ files. Functions are implemented in Java and called via rJava. Parallel implementation that operates directly on input FASTA/FASTQ files for fast execution.

Author: Anestis Gkanogiannis [aut, cre]

Maintainer: Anestis Gkanogiannis <anestis at gkanogiannis.com>

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

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("metabinR")

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("metabinR")
metabinR HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Clustering, Microbiome, Sequencing, Software
Version 1.5.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License GPL-3
Depends R (>= 4.2)
Imports methods, rJava
System Requirements Java (>= 8)
URL https://github.com/gkanogiannis/metabinR
Bug Reports https://github.com/gkanogiannis/metabinR/issues
See More
Suggests BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0)
Linking To
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Build Report Build Report

Package Archives

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

Source Package metabinR_1.5.0.tar.gz
Windows Binary metabinR_1.5.0.zip
macOS Binary (x86_64) metabinR_1.5.0.tgz
macOS Binary (arm64) metabinR_1.5.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/metabinR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/metabinR
Bioc Package Browser https://code.bioconductor.org/browse/metabinR/
Package Short Url https://bioconductor.org/packages/metabinR/
Package Downloads Report Download Stats