Package: metabinR 2.0.0

Anestis Gkanogiannis

metabinR: Abundance and Compositional Based Binning of Metagenomes

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.

Authors:Anestis Gkanogiannis [aut, cre]

metabinR_2.0.0.tar.gz
metabinR_2.0.0.zip(r-4.7)metabinR_2.0.0.zip(r-4.6)metabinR_2.0.0.zip(r-4.5)
metabinR_2.0.0.tgz(r-4.6-any)metabinR_2.0.0.tgz(r-4.5-any)
metabinR_2.0.0.tar.gz(r-4.7-any)metabinR_2.0.0.tar.gz(r-4.6-any)
metabinR_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
metabinR/json (API)

# Install 'metabinR' in R:

install.packages('metabinR', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gkanogiannis/metabinr/issues

Uses libs:

openjdk– OpenJDK Java runtime, using Hotspot JIT

On BioConductor:metabinR-2.1.0(bioc 3.24)metabinR-2.0.0(bioc 3.23)

classification clustering microbiome sequencing software openjdk

4.30 score 2 stars 2 scripts 10 exports 49 dependencies

Last updated from:0524acbd86 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	210
linux-devel-x86_64	OK	383
source / vignettes	OK	444
linux-release-x86_64	OK	392
macos-release-arm64	OK	198
macos-oldrel-arm64	OK	203
windows-devel	OK	306
windows-release	OK	301
windows-oldrel	OK	294
wasm-release	OK	187

Exports:abundance_based_binning algorithm as.data.frame assignments composition_based_binning hierarchical_binning metabinR_jvm_options nClusters parameters show

Dependencies:abind backports BH Biobase BiocGenerics BiocParallel Biostrings bitops checkmate cigarillo cli codetools cpp11 crayon DelayedArray deldir formatR futile.logger futile.options generics GenomicAlignments GenomicRanges hwriter interp IRanges jpeg lambda.r lattice latticeExtra MASS Matrix MatrixGenerics matrixStats png pwalign RColorBrewer Rcpp RcppEigen Rhtslib rJava Rsamtools S4Arrays S4Vectors Seqinfo ShortRead snow SparseArray SummarizedExperiment XVector

metabinR

Rendered frommetabinR_vignette.Rmdusingknitr::rmarkdown

Last update: 2026-04-24
Started: 2022-10-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Abundance based binning on metagenomic samples	abundance_based_binning
Convert a MetabinResult to a 'data.frame'	as.data.frame,MetabinResult-method
Composition based binning on metagenomic samples	composition_based_binning
Hierarchical (ABxCB) binning on metagenomic samples	hierarchical_binning
JVM options used when metabinR loads	metabinR_jvm_options
Accessors for MetabinResult	algorithm algorithm,MetabinResult-method assignments assignments,MetabinResult-method MetabinResult-accessors nClusters nClusters,MetabinResult-method parameters parameters,MetabinResult-method
MetabinResult: binning result container	MetabinResult MetabinResult-class show,MetabinResult-method