ELMER
This package is for version 3.6 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: 3.6
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: c(person("Lijing", "Yao", role = "aut", email = "lijingya@usc.edu"), person("Ben", "Berman", role = "aut"), person("Peggy", "Farnham", role = "aut"), person("Hui", "Shen", role = "ctb"), person("Peter", "Laird", role = "ctb"), person("Simon","Coetzee", role = c("cre","ctb"), email = "Simon.Coetzee@cshs.org"), person("Tiago","Chedraoui Silva", role = c("aut")))
Maintainer: Tiago Chedraoui Silva <tiagochst at usp.br>
citation("ELMER")
):
Installation
To install this package, start R (version "3.4") 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
Reference Manual |
Details
biocViews | DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription |
Version | 2.2.7 |
In Bioconductor since | BioC 3.2 (R-3.2) (8.5 years) |
License | GPL-3 |
Depends | R (>= 3.4.0), ELMER.data |
Imports | GenomicRanges, ggplot2, reshape, grid, grDevices, graphics, methods, parallel, stats, utils, IRanges, GenomeInfoDb, S4Vectors, GenomicFeatures, TCGAbiolinks(>= 2.5.5), plyr, Matrix, dplyr, Gviz, ComplexHeatmap, circlize, MultiAssayExperiment, SummarizedExperiment, biomaRt, doParallel, downloader, ggrepel, lattice, magrittr, readr, rvest, xml2, plotly, gridExtra |
System Requirements | |
URL |
See More
Suggests | BiocStyle, knitr, testthat, DT, GenomicInteractions, webshot, rtracklayer, covr |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | TCGAbiolinksGUI |
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_2.2.7.tar.gz |
Windows Binary | ELMER_2.2.7.zip |
Mac OS X 10.11 (El Capitan) | ELMER_2.2.7.tgz |
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 |
Old Source Packages for BioC 3.6 | Source Archive |