ELMER

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of ELMER; for the stable release version, see ELMER.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Bioconductor version: Development (3.24)

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")):

Tiago Chedraoui Silva, Lijing Yao, Simon Coetzee, Peggy Farnham, Benjamin Berman. ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes. doi:10.18129/B9.bioc.ELMER, R package version 2.37.1, https://bioconductor.org/packages/ELMER.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("ELMER")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

No vignettes available
Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription
Version	2.37.1
In Bioconductor since	BioC 3.2 (R-3.2) (11 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, Seqinfo, 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
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Depends On Me
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Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/ELMER
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ELMER
Package Short Url	https://bioconductor.org/packages/ELMER/
Package Downloads Report	Download Stats