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brainGraph (version 3.0.0)

Graph Theory Analysis of Brain MRI Data

Description

A set of tools for performing graph theory analysis of brain MRI data. It works with data from a Freesurfer analysis (cortical thickness, volumes, local gyrification index, surface area), diffusion tensor tractography data (e.g., from FSL) and resting-state fMRI data (e.g., from DPABI). It contains a graphical user interface for graph visualization and data exploration, along with several functions for generating useful figures.

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Install

install.packages('brainGraph')

Monthly Downloads

622

Version

3.0.0

License

GPL-3

Issues

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Repository

https://github.com/cwatson/brainGraph

Maintainer

Christopher G Watson

Last Published

September 29th, 2020

Functions in brainGraph (3.0.0)

apply_thresholds

Threshold additional set of matrices

Create a list of brainGraph graphs

brainGraph_permute

Permutation test for group difference of graph measures

Atlas helper functions

Set graph, vertex, and edge attributes common in MRI analyses

Difference in the area-under-the-curve of two vectors

brainGraph-methods

brainGraph generic methods

Default options for brainGraph

Bootstrapping for global graph measures

Network-based statistic for brain MRI data

communicability

Calculate communicability

Calculate a vertex's leverage centrality

Check for vertex or edge attributes

Graph Data Tables

Create a data table with graph global and vertex measures

Calculate the p-value for differences in correlation coefficients

centr_betw_comm

Calculate communicability betweenness centrality

Fit General Linear Models at each vertex of a graph

Creating_Graphs_GLM

Create a graph list with GLM-specific attributes

Coordinates for data from brain atlases

GLM model selection

Model selection for bg_GLM objects

Calculate graph global, local, or nodal efficiency

Calculate correlation matrix and threshold

Fit design matrices to one or multiple outcomes

Create a design matrix for linear model analysis

Convenience function to get attributes for lists of random graphs

Plotting GLM graphs

Plot a graph with results from GLM-based analyses

Calculate vertex hubness

Mediation analysis with brain graph measures as mediator variables

Import data for structural connectivity analysis

delete_all_attr

Delete all attributes of a graph

Multi-threshold permutation correction

Creating_Graphs

Create a brainGraph object

make_auc_brainGraph

Calculate the AUC across densities of given attributes

Helper functions to set-up for GLM analyses

Calculate coefficient of variation

Select edges for re-wiring

Plot normalized rich club coefficients against degree threshold

Return a vector of filenames based on a directory name or options list

Calculate an asymmetry index based on edge counts

contract_brainGraph

Contract graph vertices based on brain lobe and hemisphere

GLM influence measures

Influence measures for a bg_GLM object

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

mean_distance_wt

Calculate weighted shortest path lengths

Extract model fit statistics from a bg_GLM object

Matrix utilities

Matrix/array utility functions

plot_brainGraph_gui

GUI for plotting graphs overlaid on an MNI152 image or in a circle

Write files to be used for visualization with BrainNet Viewer

Extract basic information from a bg_GLM object

Plot global graph measures across densities

Test if an object is a character vector of numbers

Count number of edges of a brain graph

rich_club_attrs

Assign graph attributes based on rich-club analysis

Analysis of network robustness

plot.brainGraph

Plot a brain graph with a specific spatial layout

Calculate the s-core of a network

set_graph_colors

Color graph vertices and edges

IndividualContributions

Approaches to estimate individual network contribution

plot_volumetric

Plot group distributions of volumetric measures for a given brain region

Calculate the inverse of the cross product of a design matrix

Perform an analysis with random graphs for brain MRI data

Linear model residuals in structural covariance networks

Rich club calculations

plot_vertex_measures

Plot vertex-level graph measures at a single density or threshold

Create connection matrices for tractography or fMRI data

GLM non-parametric permutation testing

Utility functions

Utility functions

Gateway coefficient, participation coefficient, and within-mod degree z-score

make_intersection_brainGraph

Create the intersection of graphs based on a logical condition

make_ego_brainGraph

Create a graph of the union of multiple vertex neighborhoods

Calculate graph small-worldness

update_fs_names

Update column names in a Freesurfer table

Subset graphs based on a given logical condition

Rename the levels of global metrics in a data.table

Graph Distances

Calculate Euclidean distance of edges and vertices

Variance inflation factors for bg_GLM objects

Calculate graph vulnerability