dorothea

This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see dorothea.

All versions

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

Collection Of Human And Mouse TF Regulons

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-1004-3923 , Daniel Dimitrov [aut] ORCID: 0000-0002-5197-2112 , Christian H. Holland [aut] ORCID: 0000-0002-3060-5786 , 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 (from within R, enter citation("dorothea")):

Daniel Dimitrov, Christian H. Holland, Luz Garcia-Alonso. dorothea: Collection Of Human And Mouse TF Regulons. doi:10.18129/B9.bioc.dorothea, R package version 1.23.0, https://bioconductor.org/packages/dorothea.

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("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	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, Homo_sapiens_Data, Mus_musculus_Data
Version	1.23.0
In Bioconductor since	BioC 3.11 (R-4.0) (6.5 years)
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

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	epiregulon.extra, MethReg, netZooR
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	dorothea_1.23.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-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