TIminer: NGS data mining pipeline for cancer immunology and immunotherapy.

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

SUBMITTER: Tappeiner E 

PROVIDER: S-EPMC5870678 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature