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("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 | ||
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | cosmosR, easier |
| Suggests Me | MethReg |
| Links To Me | |
| Build Report | Build Report |
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/ |
| Package Downloads Report | Download Stats |