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| aal116 | Coordinates for data from the AAl116 atlas |
| aal90 | Coordinates for data from the AAl90 atlas |
| analysis_random_graphs | Perform an analysis with random graphs for brain MRI data |
| aop | "Add-one-patient" approach to estimate individual network contribution |
| assign_lobes | Give vertices in a graph a _lobe_ attribute. |
| boot_global | Bootstrapping for global graph measures |
| brainGraph_init | Initialize variables for further use in brainGraph |
| brainsuite | Coordinates for data from BrainSuite atlas |
| centr_lev | Calculate a vertex's leverage centrality |
| check.resid | Check model residuals for each brain region |
| choose.edges | Select edges for re-wiring. |
| color.edges | Color graph edges |
| color.vertices | Color graph vertices |
| corr.matrix | Calculate correlation matrix and threshold |
| count_homologous | Count number of edges between homologous regions of a brain graph |
| count_interlobar | Count number of inter-lobar connections from a given major lobe |
| destrieux | Coordinates for data from the Destrieux atlas |
| destrieux.scgm | Coordinates for data from the Destrieux atlas |
| dk | Coordinates for data from the Desikan-Killiany atlas |
| dk.scgm | Coordinates for data from the Desikan-Killiany atlas |
| dkt | Coordinates for data from the Desikan-Killiany-Tourville atlas |
| dkt.scgm | Coordinates for data from the Desikan-Killiany-Tourville atlas |
| dti_create_mats | Create connection matrices for tractography analysis |
| edge_asymmetry | Calculate an asymmetry index based on edge counts |
| edge_spatial_dist | Calculate Euclidean distance of edges |
| get.resid | Linear model residuals across brain regions |
| graph.contract.brain | Contract graph vertices based on brain lobe and hemisphere |
| graph.efficiency | Calculate graph global, local, or nodal efficiency |
| graph_attr_dt | Create a data table with graph global measures |
| graph_neighborhood_multiple | Take the union of multiple neighborhood graphs |
| hoa112 | Coordinates for data from Harvard-Oxford atlas |
| loo | "Leave-one-out" approach to estimate individual network contribution |
| lpba40 | Coordinates for data from the LONI probabilistic brain atlas |
| make_empty_brainGraph | Create an empty graph with attributes for brainGraph |
| NBS | Network-based statistic for brain MRI data |
| part.coeff | Calculate vertex participation coefficient |
| permute.group | Permutation test for group difference of graph measures |
| plot_boot | Plot global graph measures with shaded regions calculated from bootstrapping |
| plot_brainGraph | Plot a graph with a specific spatial layout |
| plot_brainGraph_gui | GUI for plotting graphs overlaid on an MNI152 image or in a circle. |
| plot_brainGraph_list | Write PNG files for a list of graphs |
| plot_brainGraph_mni | Draw an axial or sagittal slice of the MNI152 T1 image |
| plot_corr_mat | Plot a correlation matrix |
| plot_global | Plot global graph measures across densities |
| plot_group_means | Plot group distributions of volumetric measures for a given brain region |
| plot_perm_diffs | Calculate permutation p-values and plot group differences |
| plot_rich_norm | Plot normalized rich club coefficients against degree threshold |
| plot_vertex_measures | Plot vertex-level graph measures at a single density |
| rich.club.coeff | Calculate the rich club of a graph |
| rich.club.norm | Calculate the normalized rich club coefficient |
| rich.core | Calculate the rich core of a graph |
| robustness | Analysis of network robustness |
| rotation | Apply a rotation matrix to a set of points |
| set.brainGraph.attributes | Set a number of graph and vertex attributes useful in MRI analyses |
| sim.rand.graph.clust | Simulate a random graph with given degree sequence and clustering. |
| sim.rand.graph.par | Simulate N random graphs w/ same clustering and degree sequence as the input. |
| small.world | Calculate graph small-worldness |
| SPM | Perform between-group tests at each vertex for a given vertex measure |
| update_brainGraph_gui | Function to dynamically plot a graph |
| vec.transform | Transform a vector to have a different range |
| vertex_attr_dt | Create a data table with graph vertex measures |
| vertex_spatial_dist | Calculate average Euclidean distance for each vertex |
| vulnerability | Calculate graph vulnerability |
| within_module_deg_z_score | Calculate vertex within-module degree z-score |
| write.brainnet | Write files to be used for visualization with BrainNet Viewer |