Perelman School of Medicine at the University of Pennsylvania

Shen Lab

Software

 

Name Description
HDBIG HDBIG is a collection of software tools for high dimensional brain imaging genomics.
HDBIG-SR An HDBIG toolkit for sparse regression with a few regularization terms, including lasso, elastic net, L21 norm, group L21 norm, and network guided L21 norm.
HDBIG-SCCA An HDBIG toolkit for sparse association discovery with a knowledge-guided regularization term.
HDBIG-S2CCA An HDBIG toolkit for structured sparse association discovery with a few Sparse Canonical Correlation Analysis (SCCA) models, including the structure-aware SCCA model (S2CCA), the GraphNet SCCA model (GN-SCCA), the Graph OSCAR SCCA (GOSC-SCCA) model, and the Absolute value based GraphNet SCCA model (AGN-SCCA).
HDBIG-SCCA-NC An HDBIG toolkit for structured sparse association discovery with a generic non-convex penalty.
HDBIG-S2CCA-TLP An HDBIG toolkit for structured sparse association discovery with a truncated l1-norm penalty.
HDBIG-IGEA An HDBIG toolkit for mining high-level imaging genetic associations via applying enrichment analysis to two dimensional imaging genetic modules.
HDBIG-NWAS-RP An HDBIG toolkit for mining high-level imaging genetic associations using tissue-specific functional networks and network GWAS reprioritization strategy.
HDBIG-IGB-W An HDBIG web interface for archiving, visualization and interactive exploration of brain imaging genetics findings.
BECA  BECA is a prototype Brain Explorer for Connectomic Analysis.
SPHARM-MAT SPHARM-MAT is a matlab-based 3D shape modeling and analysis toolkit, and is designed to aid statistical shape analysis for relating morphometric changes in 3D structures of interest to different conditions.