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>
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 | ||
| NEWS | Text |
Details
| biocViews | Clustering, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription |
| Version | 1.4.1 |
| 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, Rtsne, survival |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| 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 | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/M3C/ |
| Package Short Url | https://bioconductor.org/packages/M3C/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.8 | Source Archive |