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ELMER

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes


Bioconductor version: Release (3.19)

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 gmail.com>

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

Installation

To install this package, start R (version "4.4") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ELMER")
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 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription
Version 2.28.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 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(>= 1.61.2), DelayedArray
System Requirements
URL
See More
Suggests BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData
Linking To
Enhances
Depends On Me
Imports Me TCGAWorkflow
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_2.28.0.tar.gz
Windows Binary ELMER_2.28.0.zip (64-bit only)
macOS Binary (x86_64) ELMER_2.28.0.tgz
macOS Binary (arm64) ELMER_2.28.0.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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.19 Source Archive