- HotSpots (Updated 2016) a method to infer cancer somatic mutation hotspots, as descriibed in Qi et al 2016
- CANOES, (Updated 2014) a method to call CNVs from exome sequencing data with arbitrary number of reference samples.
- Repertoire, (Updated 2015) Scripts for analyzing T cell receptor repertoire sequencing data.
- OPERA , (updated 2012) an online power calculator for genome sequencing and genetic studies
- Zinfandel, (updated 2012) calling Copy Number Variants (CNVs) from whole genome data based on both depth of coverage and mate pair information
- Atlas-SNP, (last updated 2010) bioinformatics analysis of next-generation sequencing, optimized for variant calling from 454 data
- Genometer, (last updated 2011) estimating genome size in the presence of repeats
Homsy et al, Science, 2015: de novo mutations from 1120 congenital heart disease cases
- S1: Phenotypes for each case proband, including cardiac, neurodevelopmental disorders and extra-cardiac congenital anomalies.
- S2: List of de novo Mutations in CHD case cohort.
- S3: List of de novo Mutations in Control cohort.
- S4: List of de novo probabilities for each variant class in each protein-coding gene on the Nimblegen V2 exome, adjusted for depth in Cases.
- S5: List of de novo probabilities for each variant class in each protein-coding gene on the Nimblegen V2 exome, adjusted for depth in Controls.
- S6: Functional term enrichment analysis of all Genes with Damaging (loss of function + deleterious missense) de novo mutations in all cases.
- S7: Functional term enrichment analysis of all Genes with Loss of Function de novo mutations in 860 new cases.
- S8: List of 1,563 variants (1,161 unique genes) with damaging de novo mutations from 7 independent NDD cohorts.
- S9: Functional term enrichment analysis among 69 genes with Damaging de novo mutations overlapping between CHD cases and the published NDD (P-NDD) cohort.
- S10: Percentile ranks of genes by expression in the developing mouse heart and brain.
GWAS of drug adverse reactions
GWAS data sets from Serious Adverse Event Consortium, related to these papers (Daly et al 2009; Shen et al 2011; Lucena et al 2011; Overby et al 2014) can be found at SAEC Data Portal (Registration required). Processed files ready for PLINK are available upon request (email@example.com).