M3C

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see M3C.

Monte Carlo Consensus Clustering


Bioconductor version: 3.7

Genome-wide data is used to stratify patients into classes using class discovery algorithms. However, we have observed systematic bias present in current state-of-the-art methods. This arises from not considering reference distributions while selecting the number of classes (K). As a solution, we developed a consensus clustering-based algorithm with a hypothesis testing framework called Monte Carlo consensus clustering (M3C). M3C uses a multi-core enabled Monte Carlo simulation to generate null distributions along the range of K which are used to calculate p values to select its value. P values beyond the limits of the simulation are estimated using a beta distribution. M3C can quantify structural relationships between clusters and uses spectral clustering to deal with non-gaussian and imbalanced structures.

Author: Christopher John [aut, cre]

Maintainer: Christopher John <chris.r.john86 at gmail.com>

Citation (from within R, enter citation("M3C")):

Installation

To install this package, start R (version "3.5") and enter:


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

BiocManager::install("M3C")

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("M3C")
M3C HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, GeneExpression, RNASeq, Sequencing, Software, Transcription
Version 1.2.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License AGPL-3
Depends R (>= 3.4.0)
Imports ggplot2, Matrix, doSNOW, NMF, RColorBrewer, cluster, parallel, foreach, doParallel, matrixcalc, dendextend, sigclust
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Suggests knitr, rmarkdown
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Package Archives

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

Source Package M3C_1.2.0.tar.gz
Windows Binary M3C_1.2.0.zip
Mac OS X 10.11 (El Capitan) M3C_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/M3C
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/M3C
Package Short Url https://bioconductor.org/packages/M3C/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive