dorothea

DOI: 10.18129/B9.bioc.dorothea    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see dorothea.

Collection Of Human And Mouse TF Regulons

Bioconductor version: 3.13

This package contains human and mouse TF regulons. The human regulons were curated and collected from different types of evidence such as literature curated resources, ChIP-seq peaks, TF binding site motifs and interactions inferred directly from gene expression. The mouse regulons were constructed by mapping the human gene symbols to their orthologs in mice. Those regulons can be coupled with any statistical method that aims to analyse gene sets to infer TF activity from gene expression data. Preferably the statistical method viper is used.

Author: Christian H. Holland [cre, aut] , Luz Garcia-Alonso [aut], Alberto Valdeolivas [ctb], Minoo Ashtiani [ctb], Attila Gabor [ctb]

Maintainer: Christian H. Holland <cholland2408 at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	TF activity inference from bulk transcriptomic data with DoRothEA as regulon resource.
HTML	R Script	TF activity inference from scRNA-seq data with DoRothEA as regulon resource.
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	ExperimentData, Homo_sapiens_Data, Mus_musculus_Data
Version	1.4.2
License	GPL-3 + file LICENSE
Depends	R (>= 4.0)
Imports	dplyr, magrittr, bcellViper, viper
LinkingTo
Suggests	Biobase, BiocStyle, 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
Suggests Me	MethReg
Links To Me
Build Report

Package Archives

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

Source Package	dorothea_1.4.2.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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