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TIminer / Tumor Immunology miner

Performs integrative immunogenomic analyses using next generation sequencing (NGS) data. TIminer analyzes single-sample RNA-seq data and somatic DNA mutations to characterize the tumor-immune interface. It is able to: (1) provide genotypes human leukocyte antigens (HLAs) from NGS data, (2) predict tumor neoantigens using mutation data and HLA types, (3) characterize tumor-infiltrating immune cells from bulk RNA-seq data; and (4) quantify tumor immunogenicity from expression data.

Hapl-o-Mat

Allows human leucocyte antigen (HLA) haplotype frequency estimation. Hapl-o-Mat preprocesses the input genotype data, resolves genotyping ambiguities, translates alleles to a uniform resolution per locus and then computes the most likely set of haplotypes including their frequencies via the expectation-maximization (EM) algorithm. The software handles large-scale HLA genotype data. Its accuracy and performance were demonstrated on the basis of artificial and real genotype data.