lionessR

DOI: 10.18129/B9.bioc.lionessR    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see lionessR.

Modeling networks for individual samples using LIONESS

Bioconductor version: 3.14

LIONESS, or Linear Interpolation to Obtain Network Estimates for Single Samples, can be used to reconstruct single-sample networks (https://arxiv.org/abs/1505.06440). This code implements the LIONESS equation in the lioness function in R to reconstruct single-sample networks. The default network reconstruction method we use is based on Pearson correlation. However, lionessR can run on any network reconstruction algorithms that returns a complete, weighted adjacency matrix. lionessR works for both unipartite and bipartite networks.

Author: Marieke Lydia Kuijjer [aut] , Ping-Han Hsieh [cre]

Maintainer: Ping-Han Hsieh <dn070017 at gmail.com>

Installation

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

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

BiocManager::install("lionessR")

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("lionessR")

 

HTML	R Script	lionessR
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneExpression, Network, NetworkInference, Software
Version	1.8.0
In Bioconductor since	BioC 3.10 (R-3.6) (2.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.6.0)
Imports	stats, SummarizedExperiment, S4Vectors
LinkingTo
Suggests	knitr, rmarkdown, igraph, reshape2, limma
SystemRequirements
Enhances
URL	https://github.com/mararie/lionessR
BugReports	https://github.com/mararie/lionessR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	lionessR_1.8.0.tar.gz
Windows Binary	lionessR_1.8.0.zip
macOS 10.13 (High Sierra)	lionessR_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/lionessR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/lionessR
Package Short Url	https://bioconductor.org/packages/lionessR/
Package Downloads Report	Download Stats