Software

Genomic prediction of phenotype 

Screen Shot 2015-07-11 at 6.48.49 pmSparSNP – Regularized linear models of genetic data for phenotype prediction
BMC Bioinformatics 2012 | Code

 

Analysis of multi-omics data

Screen Shot 2015-07-11 at 6.18.43 pmflashpca – Biobank-scale principal components analysis and canonical correlation analysis
flashpca1: PLoS One, 2014 | flashpca2: Bioinformatics, 2017 | Code

 

NetRep
• NetRep – Replication and preservation testing of omics networks
Cell Systems, 2016 | Code

 

BootstrapQTL2BootstrapQTL – Quantitative trait locus mapping tool with accurate effect size estimates
BioRxiv, 2017 | Code

 

Screen Shot 2015-07-11 at 6.23.32 pm
Illuminus – Accurate genotype calling for the Illumina platform
Bioinformatics, 2007 | Code

 

Sequence analysis

Screen Shot 2015-07-11 at 6.43.33 pmSRST2 – Genomic surveillance of bacterial pathogens
Genome Medicine 2014 | Code | Illumina BaseSpace | Behind the SRST2 project