mosbi
Molecular Signature identification using Biclustering
Bioconductor version: Release (3.20)
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("mosbi")):
Installation
To install this package, start R (version "4.4") 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")| example-workflow | HTML | R Script |
| similarity-metrics-evaluation | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, Network, Software, StatisticalMethod |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 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_1.12.0.tar.gz |
| Windows Binary (x86_64) | mosbi_1.12.0.zip (64-bit only) |
| macOS Binary (x86_64) | mosbi_1.12.0.tgz |
| macOS Binary (arm64) | mosbi_1.12.0.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 |