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https://www.selleckchem.com/products/pyrintegrin.html J Res Proteome 161806-1816, 2017).OpenVax is a computational workflow for identifying somatic variants, predicting neoantigens, and selecting the contents of personalized cancer vaccines. It is a Dockerized end-to-end pipeline that takes as input raw tumor/normal sequencing data. It is currently used in three clinical trials (NCT02721043, NCT03223103, and NCT03359239). In this chapter, we describe how to install and use OpenVax, as well as how to interpret the generated results.Tumor neoantigens are at the core of immunological tumor control and response to immunotherapy. In silico prediction of tumor neoantigens from next-generation sequencing (NGS) data is possible but requires the assembly of complex, multistep computational pipelines and extensive data preprocessing. Using public data from two cancer cell lines, here we show how TIminer, a framework to perform immunogenomics analyses, can be easily used to assemble and run customized pipelines to predict cancer neoantigens from multisample NGS data.MHCflurry is an open source package for peptide/MHC I binding affinity prediction. Its command-line and programmatic interfaces make it well-suited for integration into high-throughput bioinformatic pipelines. Users can download models fit to publicly available data or train predictors on their own affinity measurements or mass spec datasets. This chapter gives a tutorial on essential MHCflurry functionality, including generating predictions, training new models, and using the MHCflurry Python interface. MHCflurry is available at https//github.com/openvax/mhcflurry .The plethora of RNA-seq data which have been generated in the recent years constitutes an attractive resource to investigate HLA variation and its relationship with normal and disease phenotypes, such as cancer. However, next generation sequencing (NGS) brings new challenges to HLA analysis because of the mapping bias introduced by aligning short reads

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