dorothea
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see dorothea.
Collection Of Human And Mouse TF Regulons
Bioconductor version: 3.19
DoRothEA is a gene regulatory network containing signed transcription factor (TF) - target gene interactions. DoRothEA regulons, the collection of a TF and its transcriptional targets, were curated and collected from different types of evidence for both human and mouse. A confidence level was assigned to each TF-target interaction based on the number of supporting evidence.
Author: Pau Badia-i-Mompel [cre] 
, Daniel Dimitrov [aut] , Christian H. Holland [aut] , Luz Garcia-Alonso [aut], Alberto Valdeolivas [ctb], Minoo Ashtiani [ctb], Attila Gabor [ctb]
Maintainer: Pau Badia-i-Mompel <pau.badia at uni-heidelberg.de>
citation("dorothea")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("dorothea")
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("dorothea")| DoRothEA regulons. | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ExperimentData, Homo_sapiens_Data, Mus_musculus_Data |
| Version | 1.16.0 |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.0) |
| Imports | dplyr, magrittr, bcellViper, decoupleR |
| System Requirements | |
| URL | https://saezlab.github.io/dorothea/ https://github.com/saezlab/dorothea |
| Bug Reports | https://github.com/saezlab/dorothea/issues |
See More
| Suggests | Biobase, BiocStyle, OmnipathR, viper, knitr, pheatmap, pkgdown, rmarkdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | cosmosR, easier |
| Suggests Me | MethReg, epiregulon.extra |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | dorothea_1.16.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/dorothea |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/dorothea |
| Package Short Url | https://bioconductor.org/packages/dorothea/ |
| Package Downloads Report | Download Stats |