lionessR
This is the released version of lionessR; for the devel version, see lionessR.
Modeling networks for individual samples using LIONESS
Bioconductor version: Release (3.23)
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("lionessR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| lionessR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, Network, NetworkInference, Software |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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_1.26.0.tar.gz |
| Windows Binary (x86_64) | lionessR_1.26.0.zip |
| macOS Binary (big-sur-x86_64) | lionessR_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | lionessR_1.26.0.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 |