FEM

DOI: 10.18129/B9.bioc.FEM    

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

Identification of Functional Epigenetic Modules

Bioconductor version: 3.8

The FEM package performs a systems-level integrative analysis of DNA methylation and gene expression data. It seeks modules of functionally related genes which exhibit differential promoter DNA methylation and differential expression, where an inverse association between promoter DNA methylation and gene expression is assumed. For full details, see Jiao et al Bioinformatics 2014.

Author: Andrew E. Teschendorff and Zhen Yang

Maintainer: Zhen Yang <yangzhen at picb.ac.cn>

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("FEM")

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("FEM")

 

PDF	R Script	The FEM package performs a systems-level integrative analysis of DNA methylationa and gene expression. It seeks modules of functionally related genes which exhibit differential promoter DNA methylation and differential expression, where an inverse association between promoter DNA methylation and gene expression is assumed. For full details, see Jiao et al Bioinformatics 2014.
PDF		Reference Manual

Details

biocViews	DifferentialExpression, DifferentialMethylation, NetworkEnrichment, Software, SystemsBiology
Version	3.10.0
In Bioconductor since	BioC 3.0 (R-3.1) (4.5 years)
License	GPL (>=2)
Depends	AnnotationDbi, Matrix, marray, corrplot, igraph, impute, limma, org.Hs.eg.db, graph, BiocGenerics
Imports	graph
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SystemRequirements
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Depends On Me	ChAMP
Imports Me
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Build Report

Package Archives

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

Source Package	FEM_3.10.0.tar.gz
Windows Binary	FEM_3.10.0.zip
Mac OS X 10.11 (El Capitan)	FEM_3.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FEM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/FEM
Package Short Url	http://bioconductor.org/packages/FEM/
Package Downloads Report	Download Stats