Software & Tutorials

John Muschelli's software

brainR
whiteStripe
fslr
John's youtube channel has a lot of tutorials
John's github page has a lot of software in development

Mandy's shrinkit and shrinkR for shrinkage estimation for clustering
Shaojie Chen's pgica for parallel group ICA
Aaron Fisher's ggbrain package
Martin Lindquist's software page
We started a github repository for BRISK (Brain R Image Science Kit)
Brian Caffo's youtube channel
Colon fitting point selection software

Youtube demo

3D Slicer

Slides from Vadim, Johns Youtube tutorial

MIPAV

Elizabeth, Haochang and Taki's youtube videos

exactLoglinTest, MCMC software for exact testing of contingency table data

paper, software

Bayesian Analysis for Penalized Spline Regression
- technical report, software
Bayesian Functional Data Analysis

technical report, software

Longitudinal Functional Principal Component Analysis

paper LFPCA.r

Multilevel Functional Principal Component Analysis

paper MFPCA.r

Multilevel Sparse Functional Principal Component Analysi

paper MFPCA_sparse.r

Penalized functional regression

refund package

Longitudinal penalized functional regression

paper, lpfr function in the refund package

Penalized splines
- Exact for R/LRT of zero variance in LMMs, R/LRT null distribution MATLAB programs
- Exact for R/LRT of zero variance in LMMs, RLRsim (written by Fabian Scheipl) RLRsim R package
- Fast Adaptive Penalised Splines, JCGS 17(1), 1-20 technical report, R package
Pspline ICA

working paper, software