ELMER
This package is for version 3.19 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: 3.19
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 gmail.com>
citation("ELMER")
):
Installation
To install this package, start R (version "4.4") 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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ELMER")
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 | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription |
Version | 2.28.0 |
In Bioconductor since | BioC 3.2 (R-3.2) (9 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(>= 1.61.2), DelayedArray |
System Requirements | |
URL |
See More
Suggests | BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | TCGAWorkflow |
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_2.28.0.tar.gz |
Windows Binary (x86_64) | ELMER_2.28.0.zip |
macOS Binary (x86_64) | ELMER_2.28.0.tgz |
macOS Binary (arm64) | ELMER_2.28.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/ELMER |
Source Repository (Developer Access) | git clone [email protected]:packages/ELMER |
Bioc Package Browser | https://code.bioconductor.org/browse/ELMER/ |
Package Short Url | https://bioconductor.org/packages/ELMER/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.19 | Source Archive |