ELMER

DOI: 10.18129/B9.bioc.ELMER    

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Bioconductor version: Release (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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ELMER")

Documentation

HTML	R Script	1 - ELMER: An R/Bioconductor Tool Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Methylomes
HTML	R Script	2 - Introduction: Input data
HTML	R Script	3.1 - Data input - Creating MAE object
HTML	R Script	3.2 - Identifying differentially methylated probes
HTML	R Script	3.3 - Identifying putative probe-gene pairs
HTML	R Script	3.4 - Motif enrichment analysis on the selected probes
HTML	R Script	3.5 - Identifying regulatory TFs
HTML	R Script	3.6 - TCGA.pipe: Running ELMER for TCGA data in a compact way
HTML	R Script	4.1 - Scatter plots
HTML	R Script	4.2 - Schematic plots
HTML	R Script	4.3 - Motif enrichment plots
HTML	R Script	4.4 - Regulatory TF plots
HTML	R Script	4.5 - Heatmap plots
HTML	R Script	5 - Integrative analysis workshop with TCGAbiolinks and ELMER - Analysis GUI
PDF		Reference Manual

Details

biocViews	DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription
Version	2.2.7
In Bioconductor since	BioC 3.2 (R-3.2) (2.5 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
LinkingTo
Suggests	BiocStyle, knitr, testthat, DT, GenomicInteractions, webshot, rtracklayer, covr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	TCGAbiolinksGUI
Suggests Me
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
Package Short Url	http://bioconductor.org/packages/ELMER/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive