ELMER

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Bioconductor version: 3.23 · Package version: 2.36.0

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.

Installation

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

BiocManager::install("ELMER")

Details

Maintainer	Tiago Chedraoui Silva <tiagochst@gmail.com>
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]
License	GPL-3
Downloads rank	510
Source branch	RELEASE_3_23
biocViews	DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription

Download

Source package

Dependencies

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

Suggests: BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData