Genomic prediction of phenotype
• SparSNP – Regularized linear models of genetic data for phenotype prediction
BMC Bioinformatics 2012 | Code
Analysis of multi-omics data
• flashpca – Biobank-scale principal components analysis and canonical correlation analysis
flashpca1: PLoS One, 2014 | flashpca2: Bioinformatics, 2017 | Code
• NetRep – Replication and preservation testing of omics networks
Cell Systems, 2016 | Code
• BootstrapQTL – Quantitative trait locus mapping tool with accurate effect size estimates
BioRxiv, 2017 | Code
• Illuminus – Accurate genotype calling for the Illumina platform
Bioinformatics, 2007 | Code
Sequence analysis
• SRST2 – Genomic surveillance of bacterial pathogens
Genome Medicine 2014 | Code | Illumina BaseSpace | Behind the SRST2 project
