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mosbi

This is the development version of mosbi; for the stable release version, see mosbi.

Molecular Signature identification using Biclustering


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("mosbi")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Clustering, Network, Software, StatisticalMethod
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License AGPL-3 + file LICENSE
Depends R (>= 4.1)
Imports Rcpp, BH, xml2, methods, igraph, fabia, RcppParallel, biclust, isa2, QUBIC, akmbiclust, RColorBrewer
System Requirements C++17, GNU make
URL
See More
Suggests knitr, rmarkdown, BiocGenerics, runibic, BiocStyle, testthat (>= 3.0.0)
Linking To Rcpp, BH, RcppParallel
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package mosbi_1.9.0.tar.gz
Windows Binary mosbi_1.9.0.zip
macOS Binary (x86_64) mosbi_1.9.0.tgz
macOS Binary (arm64) mosbi_1.9.0.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