Institute for Genomic Health, Mount Sinai
Software
- Gencrypt -- A software suite that utilizes one-way cryptographic hashes in order to securely identify overlapping individuals across multiple, independent studies. Operating on PLINK .ped and .map files, Gencrypt produces a list of multiple one-way hash outputs representing different groups of SNPs. These can then be compared between datasets in order to identify identical pairs, i.e. individuals with a high percentage of one-way hashes overlapping between them, in a privacy-secure fashion.
- bmass -- Bayesian multivariate analysis of summary statistics, or bmass, is a R package that implements the Bayesian multivariate association framework from Stephens 2013 PLOS ONE. Specifically, bmass makes use of univariate genome-wide association study (GWAS) summary statistics to comprehensively explore all possible multivariate models within the framework (based on the association categories of ''Directly Associated', ''Indirectly Associated', and 'Unassociated) and identify those with the greatest amount of support. bmass is also able to combine evidence across all these multivariate models to form a single, variant-specific summary metric; from this metric bmass is able to determine the overall amount of support for declaring a variant as a new 'multivariate significant genetic association'.
- MAPITR -- MArginal ePistatis Test for Regions, or MAPITR, is a variance component model that tests for marginal epistasis -- the presence of any epistatic interactions -- between a given genetic pathway and the rest of the genome. MAPITR expects as input a set of genotypes, a single phenotype, and a list of pathways. As output, it returns for each pathway a p-value for the test against the null model of there not being any interactions between the pathway and the rest of the genome.
News:
TBD!