JoshuaTian/EpiCluster: Clustering of (epigenetic) DNA methylation data using a variational Bayes NMF algorithm
Version 0.99.0

EpiCluster is a dimensional reduction and clustering algorithm specifically designed for large DNA methylation datasets, e.g. Epigenome-Wide Association Studies (EWAS). The method is based on a variational Bayes non-negative matrix factorization (NMF) method, which preserves the bounded beta-valued nature of DNA methylation data. This NMF method is used for dimensional reduction and can be used in conjunction with the RPBMM algorithm. Users can used the algorithm for (i) dimensional reduction and inference of components of variation, (ii) for unsupervised clustering and for (iii) feature selection.

Getting started

Package details

AuthorYuan Tian [cre,aut], Andrew E Teschendorff [cre], Zhanyu Ma [cre]
Bioconductor views DimensionReduction FeatureExtraction MethylationArray Microarray
MaintainerYuan Tian <[email protected]>
LicenseGPL (>=2.00)
Version0.99.0
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("devtools")
library(devtools)
install_github("JoshuaTian/EpiCluster")
JoshuaTian/EpiCluster documentation built on Sept. 5, 2017, 9:50 a.m.