User Tools

Site Tools


Software and Datasets

We develop and maintain a variety of software, genomic annotations and web services.

Annotation Datasets

  • Roulette is a mutation rate model identifying the mutagenic effect of Polymerase III transcription at the basepair resolution.
  • shet are gene-based estimates of selection strength.

Tools for Assessment of Variants

  • PolyPhen-2 is a tool for predicting the effect of an amino acid substitution on protein structure and function, based on comparative genomics and experimentally determined protein structures. It is available as a web service, and can also be downloaded as a standalone application.
  • SNPtrack is a simple interface for mutation mapping and identifying causal mutations from whole-genome sequencing studies. It is available as a web service.

Tools for Mass Spectrometry and Proteomics

  • MS-BLAST is a tool for searching protein sequences identified with tandem mass spectrometry against databases of protein sequences. It is available as a web service and as a standalone software.

Tools for Statistical Genetics

  • Joint Likelihood Mapping (JLIM) is a tool to test for shared genetic effect between two genetic association data, for example, a disease GWAS study and gene expression QTL (eQTL) study.
  • Joint Likelihood Mapping 2 (JLIM_2.0) is a version of JLIM which supports meta-analysis across more than one cohort of matching ancestry.
  • Joint Likelihood Mapping (JLIM) 2.5 is a new version of JLIM based on summary statistics.
  • NPS is a tool for polygenic risk scoring based on partitioning-based non-parametric shrinkage algorithm.
  • RVTT is a novel statistical test of trend that assesses the relationship of the frequency of qualifying rare variants in a pathway with dichotomous disease phenotypes leveraging the Cochran-Armitage test statistic.

Tools for Cancer Genomics

  • MutPanning is designed to detect rare cancer driver genes from aggregated whole-exome sequencing data.
  • CBaSE enables cancer type and gene-specific estimation of the strength of negative and positive selection. It is available as a browser-based tool as well as for download as a standalone package.

Tools for Population Genetics

  • simDoSe is a fast and flexible Wright-Fisher simulator for arbitrary diploid selection evolving through realistic human demography.
software.txt ยท Last modified: 2023/04/28 15:25 by ivan

Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki