ELMER
This is the development version of ELMER; for the stable release version, see ELMER.
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Bioconductor version: Development (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")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("ELMER")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | DNAMethylation, GeneExpression, GeneRegulation, MotifAnnotation, Network, Software, Transcription |
| Version | 2.27.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 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 | |
| Windows Binary | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |