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 (3.21)
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] (ORCID:
Maintainer: Ping-Han Hsieh <dn070017 at gmail.com>
citation("lionessR")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, Network, NetworkInference, Software |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | lionessR_1.21.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |