ELMER

This package is for version 3.18 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: 3.18

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 "4.3") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription

Version 2.26.0

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

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_2.26.0.tar.gz

Windows Binary ELMER_2.26.0.zip (64-bit only)

macOS Binary (x86_64) ELMER_2.26.0.tgz

macOS Binary (arm64) ELMER_2.26.0.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