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lionessR

This is the development version of lionessR; for the stable release version, see lionessR.

Modeling networks for individual samples using LIONESS


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
lionessR HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneExpression, Network, NetworkInference, Software
Version 1.17.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License MIT + file LICENSE
Depends R (>= 3.6.0)
Imports stats, SummarizedExperiment, S4Vectors
System Requirements
URL https://github.com/mararie/lionessR
Bug Reports https://github.com/mararie/lionessR/issues
See More
Suggests knitr, rmarkdown, igraph, reshape2, limma
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Build Report Build Report

Package Archives

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

Source Package lionessR_1.17.0.tar.gz
Windows Binary lionessR_1.17.0.zip
macOS Binary (x86_64) lionessR_1.17.0.tgz
macOS Binary (arm64) lionessR_1.17.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/lionessR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/lionessR
Bioc Package Browser https://code.bioconductor.org/browse/lionessR/
Package Short Url https://bioconductor.org/packages/lionessR/
Package Downloads Report Download Stats