SEPIRA

This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see SEPIRA.

Systems EPigenomics Inference of Regulatory Activity


Bioconductor version: 3.13

SEPIRA (Systems EPigenomics Inference of Regulatory Activity) is an algorithm that infers sample-specific transcription factor activity from the genome-wide expression or DNA methylation profile of the sample.

Author: Yuting Chen [aut, cre], Andrew Teschendorff [aut]

Maintainer: Yuting Chen <cytwarmmay at hotmail.com>

Citation (from within R, enter citation("SEPIRA")):

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SEPIRA")

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("SEPIRA")
Introduction to `SEPIRA` HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, GeneRegulation, GeneTarget, Network, NetworkInference, Software, Transcription
Version 1.12.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-3
Depends R (>= 3.5.0)
Imports limma(>= 3.32.5), corpcor (>= 1.6.9), parallel (>= 3.3.1), stats
System Requirements
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Suggests knitr, rmarkdown, testthat, igraph
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SEPIRA_1.12.0.tar.gz
Windows Binary SEPIRA_1.12.0.zip
macOS 10.13 (High Sierra) SEPIRA_1.12.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/SEPIRA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SEPIRA
Bioc Package Browser https://code.bioconductor.org/browse/SEPIRA/
Package Short Url https://bioconductor.org/packages/SEPIRA/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.13 Source Archive