Atlas Helpers           Atlas helper functions
Attributes              Set graph, vertex, and edge attributes common
                        in MRI analyses
Bootstrapping           Bootstrapping for global graph measures
Brain Atlases           Coordinates for data from brain atlases
Count Edges             Count number of edges of a brain graph
Creating_Graphs         Create a brainGraph object
Creating_Graphs_GLM     Create a graph list with GLM-specific
                        attributes
GLM                     Fit General Linear Models at each vertex of a
                        graph
GLM basic info          Extract basic information from a bg_GLM object
GLM design              Create a design matrix for linear model
                        analysis
GLM fits                Fit design matrices to one or multiple outcomes
GLM influence measures
                        Influence measures for a bg_GLM object
GLM model selection     Model selection for bg_GLM objects
GLM statistics          Extract model fit statistics from a bg_GLM
                        object
Graph Data Tables       Create a data table with graph global and
                        vertex measures
Graph Distances         Calculate Euclidean distance of edges and
                        vertices
IndividualContributions
                        Approaches to estimate individual network
                        contribution
Inverse                 Calculate the inverse of the cross product of a
                        design matrix
Matrix utilities        Matrix/array utility functions
Mediation               Mediation analysis with brain graph measures as
                        mediator variables
NBS                     Network-based statistic for brain MRI data
Plotting GLM graphs     Plot a graph with results from GLM-based
                        analyses
Random Graphs           Perform an analysis with random graphs for
                        brain MRI data
Residuals               Linear model residuals in structural covariance
                        networks
Rich Club               Rich club calculations
Vertex Roles            Gateway coefficient, participation coefficient,
                        and within-mod degree z-score
apply_thresholds        Threshold additional set of matrices
brainGraph              Default options for brainGraph
brainGraph-methods      brainGraph generic methods
brainGraphList          Create a list of brainGraph graphs
brainGraph_permute      Permutation test for group difference of graph
                        measures
centr_betw_comm         Calculate communicability betweenness
                        centrality
centr_lev               Calculate a vertex's leverage centrality
check_sID               Test if an object is a character vector of
                        numbers
coeff_var               Calculate coefficient of variation
communicability         Calculate communicability
contract_brainGraph     Contract graph vertices based on brain lobe and
                        hemisphere
cor.diff.test           Calculate the p-value for differences in
                        correlation coefficients
corr.matrix             Calculate correlation matrix and threshold
create_mats             Create connection matrices for tractography or
                        fMRI data
edge_asymmetry          Calculate an asymmetry index based on edge
                        counts
efficiency              Calculate graph global, local, or nodal
                        efficiency
hubness                 Calculate vertex hubness
import_scn              Import data for structural connectivity
                        analysis
make_auc_brainGraph     Calculate the AUC across densities of given
                        attributes
make_ego_brainGraph     Create a graph of the union of multiple vertex
                        neighborhoods
make_intersection_brainGraph
                        Create the intersection of graphs based on a
                        logical condition
mean_distance_wt        Calculate weighted shortest path lengths
mtpc                    Multi-threshold permutation correction
plot.brainGraph         Plot a brain graph with a specific spatial
                        layout
plot.brainGraphList     Plot a brainGraphList and write to PDF
plot_brainGraph_multi   Save PNG of one or three views for all graphs
                        in a brainGraphList
plot_global             Plot global graph measures across densities
plot_rich_norm          Plot normalized rich club coefficients against
                        degree threshold
plot_vertex_measures    Plot vertex-level graph measures at a single
                        density or threshold
plot_volumetric         Plot group distributions of volumetric measures
                        for a given brain region
randomise               GLM non-parametric permutation testing
rich_club_attrs         Assign graph attributes based on rich-club
                        analysis
robustness              Analysis of network robustness
s_core                  Calculate the s-core of a network
small.world             Calculate graph small-worldness
vif.bg_GLM              Variance inflation factors for 'bg_GLM' objects
vulnerability           Calculate graph vulnerability
write_brainnet          Write files to be used for visualization with
                        BrainNet Viewer
