covr, testthat, knitr, rmarkdown, ape, RSiena, survival

Network Generator for Combinatorial Graph Problems
Methods for the generation of a wide range of network geographies, e.g., grid networks or clustered networks. Useful for the generation of benchmarking instances for the investigation of, e.g., Vehicle-Routing-Problems or Travelling Salesperson Problems.

ggplot2, lpSolve, igraph (>= 0.7.1), stringr (>= 0.6.2)

Methods for the generation of a wide range of network geographies,
e.g., grid networks or clustered networks. Useful for the generation of
benchmarking instances for the investigation of, e.g., Vehicle-Routing-Problems
or Travelling Salesperson Problems.

Functions for carrying out Network-based Gene Set Analysis by
incorporating external information about interactions among genes, as well
as novel interactions learned from data
cvTools, corpcor, glasso, glmnet, igraph

The netgsa-package contains functions for carrying out Network-based Gene Set Analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data.

Carry out Network-based Gene Set Analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data.

graph, graphite, corpcor, dplyr, glmnet, glassoFast, igraph,
Matrix, msigdbr, quadprog, rlang, magrittr

c(
person("Michael", "Hellstern", email = "mikeh1@uw.edu", role = c("aut","cre")),
person("Ali", "Shojaie", email = "ashojaie@uw.edu", role = c("aut")),
person("Jing", "Ma", role = "aut"),
person("Kun", "Yue", role = "aut"))
Carry out network-based gene set analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data. Implements methods described in Shojaie A, Michailidis G (2010) <doi:10.1093/biomet/asq038>, Shojaie A, Michailidis G (2009) <doi:10.1089/cmb.2008.0081>, and Ma J, Shojaie A, Michailidis G (2016) <doi:10.1093/bioinformatics/btw410>.
AnnotationDbi, corpcor, data.table, dplyr, genefilter, graph,
graphite, glmnet, glassoFast, httr, igraph, jsonlite, magrittr,
Matrix, msigdbr, ndexr, org.Hs.eg.db, quadprog, RCy3, reshape2,
rlang, Rcpp (>= 1.0.2)
Michael Hellstern [aut, cre],
Ali Shojaie [aut],
Jing Ma [aut],
Kun Yue [aut]