ELMER
This is the released version of ELMER; for the devel version, see ELMER.
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Bioconductor version: Release (3.23)
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")):Tiago Chedraoui Silva, Lijing Yao, Simon Coetzee, Peggy Farnham, Benjamin Berman. ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes. doi:10.18129/B9.bioc.ELMER, R package version 2.35.1, https://bioconductor.org/packages/ELMER.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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")| "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 |
| 5 - Integrative analysis workshop with TCGAbiolinks and ELMER - Analysis GUI | HTML | R Script |
| "3.4 - Motif enrichment analysis on the selected probes" | HTML | R Script |
| "3.5 - Identifying regulatory TFs" | 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 |
| "2 - Introduction: Input data" | HTML | R Script |
| "3.6 - TCGA.pipe: Running ELMER for TCGA data in a compact way" | HTML | R Script |
| "4.5 - Heatmap plots" | HTML | R Script |
| "4.3 - Motif enrichment plots" | HTML | R Script |
| "4.1 - Scatter plots" | HTML | R Script |
| "4.2 - Schematic plots" | HTML | R Script |
| "4.4 - Regulatory TF plots" | HTML | R Script |
| "11 - ELMER: Use case" | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription |
| Version | 2.35.1 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 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, Seqinfo, 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ELMER_2.35.1.tar.gz |
| Windows Binary (x86_64) | ELMER_2.35.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | ELMER_2.35.1.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 |