This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see M3C.
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>
Citation (from within R,
enter citation("M3C")
):
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.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("M3C")
HTML | R Script | M3C |
Reference Manual | ||
Text | NEWS |
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 |
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 |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: