SEPIRA (Systems EPigenomics Inference of Regulatory Activity)
SEPIRA is a novel algorithm which estimates transcription factor activity in any given sample from its genome-wide mRNA expression or DNA methylation profile(Chen Y, Widschwendter M, and Teschendorff AE 2017). It encompasses two main steps: 1.Construction of a tissue-specific transcription factor regulatory network, consisting of transcription factors that are more highly expressed in the user-specified tissue type (the ‘tissue type of interest’) compared to other tissue types, plus an associated set of high-confidence downstream targets. 2.Estimation of transcription factor activity in this network, in any given dataset consisting of gene expression or promoter DNA methylation profiles.
Maintainer: Yuting Chen
Citation
Yuting Chen, Martin Widschwendter, Andrew E.Teschendorff. 2017. “Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development.” Genome biology, 18(1), 236.
Installation
To install this package, start R (version "3.5") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SEPIRA", version = "3.8"Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SEPIRA")HTML: Introduction to SEPIRA