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 (3.24)
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. Inputs may be file paths or Biostrings/ShortRead sequence objects; results are returned as a MetabinResult S4 object wrapping cluster assignments, algorithm parameters, and input metadata.
Author: Anestis Gkanogiannis [aut, cre] 
Maintainer: Anestis Gkanogiannis <anestis at gkanogiannis.com>
citation("metabinR")):Anestis Gkanogiannis. metabinR: Abundance and Compositional Based Binning of Metagenomes. doi:10.18129/B9.bioc.metabinR, R package version 2.1.1, https://bioconductor.org/packages/metabinR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | Classification, Clustering, Microbiome, Sequencing, Software |
| Version | 2.1.1 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 years) |
| License | GPL-3 |
| Depends | R (>= 4.4), methods |
| Imports | BiocGenerics, BiocParallel, Biostrings, checkmate, cli, rJava, S4Vectors, ShortRead, utils |
| System Requirements | Java (>= 11) |
| URL | https://github.com/gkanogiannis/metabinR |
| Bug Reports | https://github.com/gkanogiannis/metabinR/issues |
See More
| Suggests | BiocStyle, covr, cvms, data.table, dplyr, ggplot2, gridExtra, knitr, R.utils, rmarkdown, sabre, spelling, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | metabinR_2.1.1.tar.gz |
| Windows Binary (x86_64) | metabinR_2.1.1.zip |
| macOS Binary (big-sur-x86_64) | metabinR_2.1.1.tgz |
| macOS Binary (sonoma-arm64) | metabinR_2.1.1.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 |