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 (3.24)
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("dorothea")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("dorothea")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | ExperimentData, Homo_sapiens_Data, Mus_musculus_Data |
| Version | 1.25.0 |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.0) |
| Imports | dplyr, magrittr, bcellViper, decoupleR |
| 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, OmnipathR, viper, knitr, pheatmap, pkgdown, rmarkdown, Seurat, SingleCellExperiment, SummarizedExperiment, testthat (>= 2.1.0), tibble, tidyr, utils |
| Linking To | |
| Enhances | |
| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-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/ |
| Package Downloads Report | Download Stats |