Network-Based Gene Set Analysis
Bayesian information criterion to select the tuning parameters for `ne...
A data frame of edges, each row corresponding to one edge
Format cytoscape nested networks
The vector of class indicators
Constrained estimation of directed networks
Constrained estimation of undirected networks
Network-Based Gene Set Analysis
Network-based Gene Set Analysis
"Quick" Network-based Gene Set Analysis
A data frame of nonedges, each row corresponding to one negative edge
Estimate optimal gene clustering structure
Obtain edgelist from graphite databases. To be used within prepareAdjM...
A list of KEGG pathways
Matrix with pathway indicators
Generates NetGSA plots
Construct adjacency matrices from graphite databases and/or user provi...
Combine edges from databases into a data.table
Data matrix p by n
Zoom in on pathway in igraph
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>.