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 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
- Chen Y, Widschwendter M, Teschendorff AE. Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development. Genome Biol 2017 Dec 20;18(1):236.
Installation
To install this package, start R 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