Software

Statistical software

• oligoClasses: infrastructure for crlmm and oligo packages for genotyping SNPs and copy number estimation from Illumina/Affymetrix arrays

• crlmm: Methods for calling genotypes and copy number for Affymetrix and Illumina genotyping platforms

• VanillaICE: A hidden Markov model for inferring copy number alterations from genotyping arrays

• XDE: A Bayesian hierarchical model for cross-study differential gene expression

• MinimumDistance: Methods for calling de novo copy number variants in case-parent trios

• CNPBayes: a Bayesian hierarchical model for copy number estimation and integration with cancer risk models

• trellis: Identification of somatic structural variants from tumor-only whole genome sequencing.