It is known that some mutant peptides, such as those resulting from missense mutations and frameshift insertions, can bind to the major histocompatibility complex and be presented to antitumor T-cells on the surface of a tumor cell. These peptides are termed neoantigen and it is important to understand this process for cancer immunotherapy. Here, we introduce an R package termed Neoantimon that can predict a list of potential neoantigens from a variety of mutations, which include not only somatic point mutations but insertions, deletions, and structural variants. Beyond the existing applications, Neoantimon is capable of attaching and reflecting several additional information, e.g., wild-type binding capability, allele specific RNA expression levels, single nucleotide polymorphism information, and combinations of mutations to filter out infeasible peptides as neoantigen.

中文翻译：

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Neoantimon：用于鉴定肿瘤特异性新抗原的多功能R包

已知某些突变肽，例如由错义突变和移码插入产生的那些，可以结合主要的组织相容性复合物，并被呈递给肿瘤细胞表面的抗肿瘤T细胞。这些肽被称为新抗原，了解这一过程对于癌症免疫疗法很重要。在这里，我们介绍了一个称为Neoantimon的R包，它可以从各种突变中预测潜在的新抗原列表，这些突变不仅包括体细胞点突变，还包括插入，缺失和结构变异。除了现有的应用程序之外，Neoantimon还能够附加和反映一些其他信息，例如，野生型结合能力，等位基因特异性RNA表达水平，单核苷酸多态性信息以及突变组合以滤除不可行的肽作为新抗原。