SEMace                  Compute the Average Causal Effect (ACE) for a
                        given source-sink pair
SEMbap                  Bow-free covariance search and data
                        de-correlation
SEMdag                  Estimate a DAG from an input (or empty) graph
SEMdci                  SEM-based differential network analysis
SEMgsa                  SEM-based gene set analysis
SEMpath                 Search for directed or shortest paths between
                        pairs of source-sink nodes
SEMrun                  Fit a graph as a Structural Equation Model
                        (SEM)
SEMtree                 Tree-based structure learning methods
Shipley.test            Missing edge testing implied by a DAG with
                        Shipley's basis-set
alsData                 Amyotrophic Lateral Sclerosis (ALS) dataset
ancestry                Node ancestry utilities
clusterGraph            Topological graph clustering
clusterScore            Module scoring
colorGraph              Vertex and edge graph coloring on the base of
                        fitting
cplot                   Subgraph mapping
dagitty2graph           Graph conversion from dagitty to igraph
extractClusters         Cluster extraction utility
factor.analysis         Factor analysis for high dimensional data
gplot                   Graph plotting with renderGraph
graph2dag               Convert directed graphs to directed acyclic
                        graphs (DAGs)
graph2dagitty           Graph conversion from igraph to dagitty
graph2lavaan            Graph to lavaan model
kegg                    KEGG interactome
kegg.pathways           KEGG pathways
lavaan2graph            lavaan model to graph
loadPathways            Import pathways and generate a reference
                        network
localCI.test            Conditional Independence (CI) local tests of an
                        acyclic graph
mergeNodes              Graph nodes merging by a membership attribute
modelSearch             Optimal model search strategies
orientEdges             Assign edge orientation of an undirected graph
pairwiseMatrix          Pairwise plotting of multivariate data
parameterEstimates      Parameter Estimates of a fitted SEM
pathFinder              Perturbed path search utility
properties              Graph properties summary and graph
                        decomposition
resizeGraph             Interactome-assisted graph re-seizing
sachs                   Sachs multiparameter flow cytometry data and
                        consensus model
summary.GGM             GGM model summary
summary.RICF            RICF model summary
transformData           Transform data methods
weightGraph             Graph weighting methods
