signet: Selection Inference in Gene NETworks

The signet R package implements a method to detect selection in biological pathways. The general idea is to search for gene subnetworks within biological pathways that present unusual features, using a heuristic approach (simulated annealing). Details about the algorithm can be found in Gouy et al. (2017).

Installation

signet is available on Bioconductor.

source("https://bioconductor.org/biocLite.R")
biocLite("signet")

You can also install the development version:

## install devtools and signet dependencies
# install.packages('devtools')
# if (!requireNamespace("BiocManager", quietly=TRUE))
    # install.packages("BiocManager")
# BiocManager::install("graph")
# BiocManager::install("RBGL")
# install.packages("igraph")

devtools::install_github('CMPG/signet')
library(signet)

Usage

You can browse signet vignette to learn how to use the package with a walkthrough example.

library(signet)
vignette("signet")

Citation

Please cite this paper if you use signet for your project:

• Gouy A, Daub JT & Excoffier L (2017) Detecting gene subnetworks under selection in biological pathways. Nucleic Acids Research 45(16): e149