ELMER
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

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ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

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.

Getting started

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

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Package details
AuthorTiago 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]
Bioconductor views DNAMethylation GeneExpression GeneRegulation MotifAnnotation Network Software Transcription
MaintainerTiago Chedraoui Silva <tiagochst@usp.br>
LicenseGPL-3
Version2.14.0
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R: 
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ELMER")

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ELMER documentation built on Nov. 8, 2020, 4:59 p.m.

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