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dorothea

Collection Of Human And Mouse TF Regulons

Bioconductor version: Release (3.17)

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 (from within R, enter citation("dorothea")):

Installation

To install this package, start R (version "4.3") 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

Details

biocViews ExperimentData, Homo_sapiens_Data, Mus_musculus_Data
Version 1.12.0
License GPL-3 + file LICENSE
Depends R (>= 4.0)
Imports dplyr, magrittr, bcellViper, decoupleR
Linking To
Suggests Biobase, BiocStyle, OmnipathR, viper, knitr, pheatmap, pkgdown, rmarkdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils
System Requirements
Enhances
URL https://saezlab.github.io/dorothea/ https://github.com/saezlab/dorothea
Bug Reports https://github.com/saezlab/dorothea/issues
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Depends On Me
Imports Me cosmosR, easier
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Package Archives

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

Source Package dorothea_1.12.0.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/
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