TIminer

TIminer is a user-friendly tool designed to help researchers analyze the interactions between tumors and immune cells from next-generation sequencing data. It enables comprehensive immunogenomic analyses, such as human leukocyte antigens typing, predicting neoantigens, characterizing immune infiltrates and quantifying tumor immunogenicity, simplifying the laborious process of assembling analytical pipelines and executing multi-step workflows.

Topic

NGS;Immunology;Allergy, clinical immunology and immunotherapeutics;Oncology

Detail

  • Operation: Sequence feature detection;Protein feature detection

  • Software interface: Command-line user interface

  • Language: Python

  • License: Various

  • Cost: Free

  • Version name: 1.0.0

  • Credit: The Austrian Science Fund, the European Unions Horizon 2020 research and innovation program, the Austrian National Bank.

  • Input: FASTQ, VCF, gzip

  • Output: txt, PDF, TSV,

  • Contact: Zlatko Trajanoski zlatko.trajanoski@i-med.ac.at

  • Collection: -

  • Maturity: Stable

Publications

  • TIminer: NGS data mining pipeline for cancer immunology and immunotherapy.
  • Tappeiner E, et al. TIminer: NGS data mining pipeline for cancer immunology and immunotherapy. TIminer: NGS data mining pipeline for cancer immunology and immunotherapy. 2017; 33:3140-3141. doi: 10.1093/bioinformatics/btx377
  • https://doi.org/10.1093/bioinformatics/btx377
  • PMID: 28633385
  • PMC: PMC5870678

Download and documentation

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