Package for single sample network reconstruction in R
LIONESS, or Linear Interpolation to Obtain Network Estimates for Single Samples, can be used to reconstruct single-sample networks (http://arxiv.org/pdf/1505.06440.pdf). This package implements the LIONESS equation in R to reconstruct single-sample networks. The default network reconstruction method we use here 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.
The easiest way to install the R package lionessR is via the devtools package from CRAN:
install.packages("devtools") library(devtools) devtools::install_github("mararie/lionessR")
And then load the package using:
Please see the vignette for an example of co-expression network analysis using lionessR. For the example, you need to have CRAN packages
reshape2 and Bioconductor package