M3C

DOI: 10.18129/B9.bioc.M3C    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see M3C.

Monte Carlo Reference-based Consensus Clustering

Bioconductor version: 3.8

Genome-wide data is used to stratify large complex datasets into classes using class discovery algorithms. A widely applied technique is consensus clustering, however; the approach is prone to overfitting and false positives. These issues arise from not considering reference distributions while selecting the number of classes (K). As a solution, we developed Monte Carlo reference-based 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 select its value. Using a reference, that maintains the correlation structure of the input features, eliminates the limitations of consensus clustering. M3C uses the Relative Cluster Stability Index (RCSI) and p values to decide on the value of K and reject the null hypothesis, K=1. M3C can also quantify structural relationships between clusters, and uses spectral clustering to deal with non-Gaussian and complex structures. M3C can automatically analyse biological or clinical data with respect to the discovered classes.

Author: Christopher John [aut, cre]

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

Installation

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

if (!requireNamespace("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")

 

HTML	R Script	M3C
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription
Version	1.4.1
In Bioconductor since	BioC 3.6 (R-3.4) (1.5 years)
License	AGPL-3
Depends	R (>= 3.4.0)
Imports	ggplot2, Matrix, doSNOW, NMF, RColorBrewer, cluster, parallel, foreach, doParallel, matrixcalc, dendextend, sigclust, Rtsne, survival
LinkingTo
Suggests	knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	M3C_1.4.1.tar.gz
Windows Binary	M3C_1.4.1.zip
Mac OS X 10.11 (El Capitan)	M3C_1.4.1.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	http://bioconductor.org/packages/M3C/
Package Downloads Report	Download Stats