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>

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


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


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


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

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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/
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Old Source Packages for BioC 3.6 Source Archive

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