dorothea

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see dorothea.

Collection Of Human And Mouse TF Regulons


Bioconductor version: 3.14

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

Maintainer: Daniel Dimitrov <daniel.dimitrov at uni-heidelberg.de>

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

Installation

To install this package, start R (version "4.1") 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")
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. HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews ExperimentData, Homo_sapiens_Data, Mus_musculus_Data
Version 1.6.0
License GPL-3 + file LICENSE
Depends R (>= 4.0)
Imports dplyr, magrittr, bcellViper, viper
System Requirements
URL https://saezlab.github.io/dorothea/ https://github.com/saezlab/dorothea
Bug Reports https://github.com/saezlab/dorothea/issues
See More
Suggests Biobase, BiocStyle, knitr, pheatmap, pkgdown, rmarkdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils
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Package Archives

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

Source Package dorothea_1.6.0.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/
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