ELMER

DOI: 10.18129/B9.bioc.ELMER    

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Bioconductor version: Release (3.7)

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>

Citation (from within R, enter citation("ELMER")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("ELMER")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ELMER")

 

HTML R Script 1 - ELMER v.2: An R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles
HTML R Script 11 - ELMER: Use case
HTML R Script 2 - Introduction: Input data
HTML R Script 3.1 - Data input - Creating MAE object
HTML R Script 3.2 - Identifying differentially methylated probes
HTML R Script 3.3 - Identifying putative probe-gene pairs
HTML R Script 3.4 - Motif enrichment analysis on the selected probes
HTML R Script 3.5 - Identifying regulatory TFs
HTML R Script 3.6 - TCGA.pipe: Running ELMER for TCGA data in a compact way
HTML R Script 4.1 - Scatter plots
HTML R Script 4.2 - Schematic plots
HTML R Script 4.3 - Motif enrichment plots
HTML R Script 4.4 - Regulatory TF plots
HTML R Script 4.5 - Heatmap plots
HTML R Script 5 - Integrative analysis workshop with TCGAbiolinks and ELMER - Analysis GUI
PDF   Reference Manual

Details

biocViews DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription
Version 2.4.4
In Bioconductor since BioC 3.2 (R-3.2) (3 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, rmarkdown, stringr
LinkingTo
Suggests BiocStyle, knitr, testthat, DT, GenomicInteractions, webshot, rtracklayer, R.utils, covr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me TCGAbiolinksGUI, TCGAWorkflow
Suggests Me
Build Report  

Package Archives

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

Source Package ELMER_2.4.4.tar.gz
Windows Binary ELMER_2.4.4.zip
Mac OS X 10.11 (El Capitan) ELMER_2.4.4.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 http://bioconductor.org/packages/ELMER/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive

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