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 (3.21)

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: ), Daniel Dimitrov [aut] (ORCID: ), Christian H. Holland [aut] (ORCID: ), 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")):

Installation

To install this package, start R (version "4.5") 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")

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

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Details

biocViews	ExperimentData, Homo_sapiens_Data, Mus_musculus_Data
Version	1.19.0
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

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
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	dorothea_1.19.0.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