DOI: 10.18129/B9.bioc.ELMER  

This package is for version 3.16 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: 3.16

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: Tiago Chedraoui Silva [aut, cre], Lijing Yao [aut], Simon Coetzee [aut], Nicole Gull [ctb], Hui Shen [ctb], Peter Laird [ctb], Peggy Farnham [aut], Dechen Li [ctb], Benjamin Berman [aut]

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

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


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HTML R Script 1 - ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles
HTML R Script 11 - ELMER: Use case
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
Text   NEWS


biocViews DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription
Version 2.22.0
In Bioconductor since BioC 3.2 (R-3.2) (7.5 years)
License GPL-3
Depends R (>= 3.4.0), ELMER.data(>= 2.9.3)
Imports GenomicRanges, ggplot2, reshape, grid, grDevices, graphics, methods, parallel, stats, utils, IRanges, GenomeInfoDb, S4Vectors, GenomicFeatures, TCGAbiolinks(>= 2.23.7), plyr, Matrix, dplyr, Gviz, ComplexHeatmap, circlize, MultiAssayExperiment, SummarizedExperiment, biomaRt, doParallel, downloader, ggrepel, lattice, magrittr, readr, scales, rvest, xml2, plotly, gridExtra, rmarkdown, stringr, tibble, tidyr, progress, purrr, reshape2, ggpubr, rtracklayer, DelayedArray
Suggests BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData
Depends On Me
Imports Me TCGAbiolinksGUI, TCGAWorkflow
Suggests Me
Links To Me
Build Report  

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Source Package ELMER_2.22.0.tar.gz
Windows Binary ELMER_2.22.0.zip
macOS Binary (x86_64) ELMER_2.22.0.tgz
macOS Binary (arm64) ELMER_2.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ELMER
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ELMER
Bioc Package Browser https://code.bioconductor.org/browse/ELMER/
Package Short Url https://bioconductor.org/packages/ELMER/
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