metabinR

DOI: 10.18129/B9.bioc.metabinR    

Abundance and Compositional Based Binning of Metagenomes

Bioconductor version: Release (3.16)

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 "4.2") 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 1.0.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License GPL-3
Depends R (>= 4.2)
Imports methods, rJava
LinkingTo
Suggests BiocStyle, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, 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_1.0.0.tar.gz
Windows Binary metabinR_1.0.0.zip (64-bit only)
macOS Binary (x86_64) metabinR_1.0.0.tgz
macOS Binary (arm64) metabinR_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/metabinR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/metabinR
Package Short Url https://bioconductor.org/packages/metabinR/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: