ELMER
This is the released version of ELMER; for the devel version, see ELMER.
All Bioconductor versions of ELMER
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Bioconductor version: 3.23 · Package version: 2.35.1
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
From within R, enter 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.
Details
| Version | 2.35.1 |
| License | GPL-3 |
| In Bioconductor since | BioC 3.2 (R-3.2) (10 years) |
| Downloads rank | 879 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription |
| Package Short Url | https://bioconductor.org/packages/ELMER/ |
Documentation
| Reference Manual | |
| NEWS | Text |
Download
Follow the 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 |
| macOS binary (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 Downloads Report | Download Stats |
Dependencies
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
Suggests: BiocStyle, AnnotationHub, ExperimentHub, knitr, testthat, data.table, DT, GenomicInteractions, webshot, R.utils, covr, sesameData