ELMER

DOI: 10.18129/B9.bioc.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 (3.17)

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>

Installation

To install this package, start R (version "4.3") 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

PDF		Reference Manual

Details

biocViews	DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription
Version	2.23.0
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
LinkingTo
Suggests	BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	TCGAWorkflow
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package
Windows Binary	ELMER_2.23.0.zip
macOS Binary (x86_64)	ELMER_2.23.0.tgz
macOS Binary (arm64)	ELMER_2.23.0.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