Software

  • LD score
  • Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.
  • PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
  • PLINK/SEQPLINK/SEQ is an open-source C/C++ library for working with human genetic variation data.
  • INRICH is a pathway analysis tool for genome wide association studies, designed for detecting enriched association signals of LD-independent genomic regions within biologically relevant gene sets.
  • GPC is an automated power analysis for variance components (VC) quantitative trait locus (QTL) linkage and association tests in sibships, and other common tests.
  • GRAIL is a tool to examine relationships between genes in different disease associated loci.
  • DAPPLE stands for Disease Association Protein-Protein Link Evaluator.
  • XHMM is a C++ software suite was written to call copy number variation (CNV) from next-generation sequencing projects, where exome capture was used (or targeted sequencing, more generally).
  • xBrowse is a software tool we use for searching for causal variants in Mendelian disease families.
  • LOFTEE is a plugin for the Ensembl Variant Effect Predictor that improves the detection and filtering of candidate protein-truncating variants.
  • igv_plotter automates the generation of IGV screenshots for sequencing reads at variant sites of interest.
  • exac_browser is the code behind our ExAC browser.
  • clinvar provides tools to parse NCBI’s ClinVar database, and a flat file representation thereof.
  • gene_lists is a collection of gene lists for genome-wide analyses.
  • minimal_representation is a collection of scripts for canonicalizing the representation of genomic variants.
  • denovolyzeR is an R package for testing the gene-wise burden of de novo variants in disease families compared to random mutational expectations.