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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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")| 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 | 2.35.1 |
| 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/ELMER/ |
| Package Short Url | https://bioconductor.org/packages/ELMER/ |
| Package Downloads Report | Download Stats |