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