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DOI: 10.18129/B9.bioc.M3C    

This is the development version of M3C; to use it, please install the devel version of Bioconductor.

Monte Carlo Consensus Clustering

Bioconductor version: Development (3.6)

A central task in genomic data analyses for stratified medicine is class discovery which is accomplished through clustering. However, an unresolved problem with current clustering algorithms is they do not test the null hypothesis and derive p values. To solve this, we developed a novel hypothesis testing framework that uses consensus clustering called Monte Carlo Consensus Clustering (M3C). M3C use a multi-core enabled Monte Carlo simulation to generate a distribution of stability scores for each number of clusters using null datasets with the same gene-gene correlation structure as the real one. These distributions are used to derive p values and a beta distribution is fitted to the data to cheaply estimate p values beyond the limits of the simulation. M3C improves accuracy, allows rejection of the null hypothesis, removes systematic bias, and uses p values to make class number decisions. We believe M3C deals with a major pitfall in current automated class discovery tools.

Author: Christopher John [aut, cre]

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

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biocViews Clustering, GeneExpression, RNASeq, Sequencing, Software, Transcription
Version 0.99.98
License AGPL-3
Depends R (>= 3.4.0)
Imports ggplot2, Matrix, doSNOW, NMF, RColorBrewer, cluster, parallel, foreach, doParallel, matrixcalc
Suggests knitr, rmarkdown
Depends On Me
Imports Me
Suggests Me
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