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ELMER

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

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ELMER")

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

Documentation

Reference Manual PDF

Details

biocViews DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription
Version 2.27.0
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
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Build Report Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (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/
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