ELMER

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see ELMER.

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Bioconductor version: 3.6

ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.

Author: c(person("Lijing", "Yao", role = "aut", email = "lijingya@usc.edu"), person("Ben", "Berman", role = "aut"), person("Peggy", "Farnham", role = "aut"), person("Hui", "Shen", role = "ctb"), person("Peter", "Laird", role = "ctb"), person("Simon","Coetzee", role = c("cre","ctb"), email = "Simon.Coetzee@cshs.org"), person("Tiago","Chedraoui Silva", role = c("aut")))

Maintainer: Tiago Chedraoui Silva <tiagochst at usp.br>

Citation (from within R, enter citation("ELMER")):

Installation

To install this package, start R (version "3.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ELMER")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription
Version	2.2.7
In Bioconductor since	BioC 3.2 (R-3.2) (8.5 years)
License	GPL-3
Depends	R (>= 3.4.0), ELMER.data
Imports	GenomicRanges, ggplot2, reshape, grid, grDevices, graphics, methods, parallel, stats, utils, IRanges, GenomeInfoDb, S4Vectors, GenomicFeatures, TCGAbiolinks(>= 2.5.5), plyr, Matrix, dplyr, Gviz, ComplexHeatmap, circlize, MultiAssayExperiment, SummarizedExperiment, biomaRt, doParallel, downloader, ggrepel, lattice, magrittr, readr, rvest, xml2, plotly, gridExtra
System Requirements
URL

Suggests	BiocStyle, knitr, testthat, DT, GenomicInteractions, webshot, rtracklayer, covr
Linking To
Enhances
Depends On Me
Imports Me	TCGAbiolinksGUI
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	ELMER_2.2.7.tar.gz
Windows Binary	ELMER_2.2.7.zip
Mac OS X 10.11 (El Capitan)	ELMER_2.2.7.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ELMER
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ELMER
Package Short Url	https://bioconductor.org/packages/ELMER/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive