metabinR

DOI: 10.18129/B9.bioc.metabinR  

Abundance and Compositional Based Binning of Metagenomes

Bioconductor version: Release (3.17)

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>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	metabinR
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Clustering, Microbiome, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
License	GPL-3
Depends	R (>= 4.2)
Imports	methods, rJava
LinkingTo
Suggests	BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0)
SystemRequirements	Java (>= 8)
Enhances
URL	https://github.com/gkanogiannis/metabinR
BugReports	https://github.com/gkanogiannis/metabinR/issues
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	metabinR_1.2.0.tar.gz
Windows Binary	metabinR_1.2.0.zip
macOS Binary (x86_64)	metabinR_1.2.0.tgz
macOS Binary (arm64)	metabinR_1.2.0.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
Old Source Packages for BioC 3.17	Source Archive