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This is the development version of dorothea; for the stable release version, see dorothea.
Bioconductor version: Development (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 <cholland2408 at gmail.com>, Luz Garcia-Alonso <cholland2408 at gmail.com>, Alberto Valdeolivas <cholland2408 at gmail.com>, Minoo Ashtiani <cholland2408 at gmail.com>, Attila Gabor <cholland2408 at gmail.com>
Maintainer: Christian H. Holland <cholland2408 at gmail.com>
Citation (from within R,
enter citation("dorothea")
):
To install this package, start R (version "4.1") 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.
Reference Manual |
biocViews | ExperimentData, Homo_sapiens_Data, Mus_musculus_Data |
Version | 1.3.0 |
License | GPL-3 + file LICENSE |
Depends | R (>= 4.0) |
Imports | dplyr, magrittr, bcellViper, viper |
LinkingTo | |
Suggests | Biobase, BiocStyle, knitr, pheatmap, pkgdown, 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 | |
Suggests Me | MethReg |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | |
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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