Software

Web Interface

GenoNet:

  • Web interface for predicting cell type specific functional consequences of non-coding variation across 127 tissues/cell types.

  • http://www.funlda.com/genonet

R Packages

KnockoffScreen

  • R-package for Identification of Putative Causal Loci in Whole-Genome Sequencing Data via Knockoff Statistics

  • A efficient knockoff generator for genetic data

  • The R package implementing KnockoffScreen is freely available to academic users. A manual provides instructions to the use of this package.

LGRF

  • R-package for the Longitudinal Genetic Random Field model (LGRF)

  • Test the association between a longitudinally measured quantitative outcome and a set of genetic variants in a gene/region

LGEWIS

  • R-package for longitudinal gene-environment-wide interaction studies

  • Single variant/set-based score tests for genetic association/gene-environment interaction in studies with time varying outcomes and environmental exposures

FSTpackage

  • R-package for unified sequence-based association tests allowing for multiple functional annotation scores

  • Individual gene / gene-set / genome-wide scan for coding and noncoding variants using summary statistics (available for meta-analysis) and functional genomics data