mosbi

DOI: 10.18129/B9.bioc.mosbi  

Molecular Signature identification using Biclustering

Bioconductor version: Release (3.16)

This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract bicluster communities from the similarity network, which can then be converted to ensemble biclusters. Additionally, MoSBi includes several network visualization methods to give an intuitive and scalable overview of the results. MoSBi comes with several biclustering algorithms, but can be easily extended to new biclustering algorithms.

Author: Tim Daniel Rose [cre, aut], Josch Konstantin Pauling [aut], Nikolai Koehler [aut]

Maintainer: Tim Daniel Rose <tim.rose at wzw.tum.de>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("mosbi")

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("mosbi")

 

HTML	R Script	example-workflow
HTML	R Script	similarity-metrics-evaluation
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, Network, Software, StatisticalMethod
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	AGPL-3 + file LICENSE
Depends	R (>= 4.1)
Imports	Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust, isa2, QUBIC, akmbiclust, RColorBrewer
LinkingTo	Rcpp, BH, RcppParallel
Suggests	knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat (>= 3.0.0)
SystemRequirements	C++17, GNU make
Enhances
URL
Depends On Me
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Build Report

Package Archives

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

Source Package	mosbi_1.4.0.tar.gz
Windows Binary	mosbi_1.4.0.zip (64-bit only)
macOS Binary (x86_64)	mosbi_1.4.0.tgz
macOS Binary (arm64)	mosbi_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mosbi
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mosbi
Bioc Package Browser	https://code.bioconductor.org/browse/mosbi/
Package Short Url	https://bioconductor.org/packages/mosbi/
Package Downloads Report	Download Stats