FEM
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see FEM.
Identification of Functional Epigenetic Modules
Bioconductor version: 3.9
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>
citation("FEM")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| 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. | R Script | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, DifferentialMethylation, NetworkEnrichment, Software, SystemsBiology |
| Version | 3.12.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | GPL (>=2) |
| Depends | AnnotationDbi, Matrix, marray, corrplot, igraph, impute, limma, org.Hs.eg.db, graph, BiocGenerics |
| Imports | graph |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | ChAMP |
| 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 | FEM_3.12.0.tar.gz |
| Windows Binary | FEM_3.12.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | FEM_3.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/FEM |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/FEM |
| Bioc Package Browser | https://code.bioconductor.org/browse/FEM/ |
| Package Short Url | https://bioconductor.org/packages/FEM/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |