ELMER

DOI: 10.18129/B9.bioc.ELMER    

This package is for version 3.15 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: 3.15

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 "4.2") 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

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
Text		NEWS

Details

biocViews	DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription
Version	2.20.0
In Bioconductor since	BioC 3.2 (R-3.2) (7 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	TCGAbiolinksGUI, TCGAWorkflow
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ELMER_2.20.0.tar.gz
Windows Binary	ELMER_2.20.0.zip
macOS Binary (x86_64)	ELMER_2.20.0.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