TIminer: NGS data mining pipeline for cancer immunology and immunotherapy


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Abstract

Summary:Recently, a number of powerful computational tools for dissecting tumor-immune cell interactions from next-generation sequencing data have been developed. However, the assembly of analytical pipelines and execution of multi-step workflows are laborious and involve a large number of intermediate steps with many dependencies and parameter settings. Here we present TIminer, an easy-to-use computational pipeline for mining tumor-immune cell interactions from next-generation sequencing data. TIminer enables integrative immunogenomic analyses, including: human leukocyte antigens typing, neoantigen prediction, characterization of immune infiltrates and quantification of tumor immunogenicity.Availability and implementation:TIminer is freely available at http://icbi.i-med.ac.at/software/timiner/timiner.shtml.Contact:zlatko.trajanoski@i-med.ac.atSupplementary information:Supplementary data are available at Bioinformatics online.

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