lionessR
This is thereleased version of lionessR; for the devel version, seelionessR.
Modeling networks for individual samples using LIONESS
Bioconductor version: Release (3.22)
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: 0000-0001-6280-3130, Ping-Han Hsieh [cre] ORCID: 0000-0003-3054-1409
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")BiocManager::install("lionessR")For older versions of R, please refer to the appropriateBioconductor 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 | 1.24.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (6 years) |
| License | MIT + fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | lionessR_1.24.0.tar.gz |
| Windows Binary (x86_64) | lionessR_1.24.0.zip |
| macOS Binary (x86_64) | lionessR_1.24.0.tgz |
| macOS Binary (arm64) | lionessR_1.24.0.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 |