dorothea

DOI: 10.18129/B9.bioc.dorothea  

This is the development version of dorothea; for the stable release version, see dorothea.

Collection Of Human And Mouse TF Regulons

Bioconductor version: Development (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>

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("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")

 

HTML	R Script	DoRothEA regulons.
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ExperimentData, Homo_sapiens_Data, Mus_musculus_Data
Version	1.15.0
License	GPL-3 + file LICENSE
Depends	R (>= 4.0)
Imports	dplyr, magrittr, bcellViper, decoupleR
LinkingTo
Suggests	Biobase, BiocStyle, OmnipathR, viper, knitr, pheatmap, pkgdown, rmarkdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils
SystemRequirements
Enhances
URL	https://saezlab.github.io/dorothea/ https://github.com/saezlab/dorothea
BugReports	https://github.com/saezlab/dorothea/issues
Depends On Me
Imports Me	cosmosR, easier
Suggests Me	MethReg
Links To Me
Build Report

Package Archives

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

Source Package	dorothea_1.15.0.tar.gz
Windows Binary
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