metabinR

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see metabinR.

Abundance and Compositional Based Binning of Metagenomes

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0002-6441-0688

Maintainer: Anestis Gkanogiannis <anestis at gkanogiannis.com>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, Clustering, Microbiome, Sequencing, Software

Version 1.10.0

In Bioconductor since BioC 3.16 (R-4.2) (3 years)

License GPL-3

Depends R (>= 4.3)

Imports methods, rJava

System Requirements Java (>= 8)

URL https://github.com/gkanogiannis/metabinR

Bug Reports https://github.com/gkanogiannis/metabinR/issues

Suggests BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0)

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Package Archives

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

Source Package metabinR_1.10.0.tar.gz

Windows Binary (x86_64) metabinR_1.10.0.zip

macOS Binary (x86_64) metabinR_1.10.0.tgz

macOS Binary (arm64) metabinR_1.10.0.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/

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