README.md

Null models in network neuroscience

Implementations of randomization and generative null models for network neuroscience, in Python, MATLAB and R.

The "live" version of Supplementary Table 1 in Null models in network neuroscience by František Váša & Bratislav Mišić.

Python

Randomization

Edges (rewiring)

• BCTpy (https://github.com/aestrivex/bctpy)

• brainconn (https://github.com/fiuneuro/brainconn)

Nodes (spin)

• NeuroMaps (https://netneurolab.github.io/neuromaps/)

Nodes (parametrized)

• BrainSMASH (https://github.com/murraylab/brainsmash)

• BrainSpace (https://brainspace.readthedocs.io)

Time-series

• pyunicorn (https://github.com/pik-copan/pyunicorn)

Correlation matrices (HQS algorithm / configuration model)

• spatiotemporal (https://github.com/mwshinn/spatiotemporal)

• scola (https://github.com/skojaku/scola)

Generative models

Edges

• neofunkatron (https://github.com/neofunkatron/neofunkatron)

Time-series

• spatiotemporal (https://github.com/mwshinn/spatiotemporal)

MATLAB

Randomization

Edges (rewiring)

• BCT (https://sites.google.com/site/bctnet)

• GRETNA (GUI) (https://nitrc.org/projects/gretna)

Nodes (spin)

• rotate_parcellation (https://github.com/frantisekvasa/rotate_parcellation)

• spin-test (vertices) (https://github.com/spin-test/spin-test)

Nodes (parametrized)

• JuSpace (https://github.com/juryxy/JuSpace)

• BrainSpace (https://brainspace.readthedocs.io)

Time-series

• Measures of Analysis of Time Series toolkit (https://mathworks.com/matlabcentral/fileexchange/27561)

• LancsBioMed (https://github.com/PhysLancIT/LancsBioMed)

Correlation matrices (HQS algorithm / configuration model)

• DDT (https://github.com/Emory-CBIS/DDT)

Correlation matrices (distance-dependence)

• spatial_fc (https://github.com/brain-networks/spatial_fc)

Graph signal processing

• Surrogate Graph Signals (https://miplab.epfl.ch/index.php/software/graph-surrogates)

Generative models

Edges

• generative_models (https://github.com/brain-networks/generative_models)

• generativenetworkmodel (https://github.com/DanAkarca/generativenetworkmodel)

R

Randomization

Edges (rewiring)

• brainGraph (https://github.com/cwatson/brainGraph)

• evalClust (https://github.com/GatesLab/evalClust)

Nodes (spin)

• rotate_parcellation (https://github.com/frantisekvasa/rotate_parcellation)

Time-series

• nonlinearTseries (https://github.com/constantino-garcia/nonlinearTseries)

Correlation matrices (HQS algorithm / configuration model)

• evalClust (https://github.com/GatesLab/evalClust)