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 (3.12)

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>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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 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 1.1.1
License GPL-3 + file LICENSE
Depends R (>= 4.0)
Imports dplyr, magrittr, bcellViper
LinkingTo
Suggests Biobase, BiocStyle, knitr, pheatmap, pkgdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils, viper
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
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package dorothea_1.1.1.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

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