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TIminer specifications

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Unique identifier OMICS_20897
Name TIminer
Alternative name Tumor Immunology miner
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Input data Some RNA-seq reads or DNA mutations.
Input format FASTQ, VCF
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Medium
Version 1.0.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Zlatko Trajanoski

Publication for Tumor Immunology miner

TIminer citations

 (3)
library_books

In silico prediction of cancer immunogens: current state of the art

2018
BMC Immunol
PMCID: 5856276
PMID: 29544447
DOI: 10.1186/s12865-018-0248-x

[…] sted on a set of 25 known tumour antigens and 25 human proteins. VaxiJen identified 96% of the test tumour antigens and 76% of the test human proteins with overall accuracy of 86% at threshold of 0.5.TIminer (Tumor Immunology miner) is a pipeline for mining tumour-immune cell interactions from next-generation sequencing data []. It provides HLA class I typing by RNA-seq, characterization of immune […]

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Neoantigens Generated by Individual Mutations and Their Role in Cancer Immunity and Immunotherapy

2017
Front Immunol
PMCID: 5712389
PMID: 29234329
DOI: 10.3389/fimmu.2017.01679

[…] se of individual steps, assembling analytical pipelines and executing workflows with a number of consecutive steps is laborious and depends on many parameter settings. The recently developed pipeline TIminer () integrates cutting-edge bioinformatics tools for the analysis of both, RNA-seq data and somatic DNA mutations in order to characterize the tumor–immune interface. This pipeline enables: (1) […]

library_books

TIminer: NGS data mining pipeline for cancer immunology and immunotherapy

2017
Bioinformatics
PMCID: 5870678
PMID: 28633385
DOI: 10.1093/bioinformatics/btx377

[…] of such analytical pipelines and execution of multi-step workflows are laborious and involves a large number of intermediate steps with many dependencies and parameter settings.We therefore developed TIminer (Tumor Immunology miner), an analytical pipeline to perform integrative immunogenomic analyses using NGS data that is easy to install and use. TIminer integrates state-of-the-art bioinformatic […]


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TIminer institution(s)
Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
TIminer funding source(s)
Supported by the Austrian Science Fund (FWF): W1101-B18 (DK Molecular Cell Biology and Oncology), the European Union’s Horizon 2020 research and innovation program under grant agreement No. 633592 (project APERIM: Advanced Bioinformatics Tools for Personalised Cancer Immunotherapy), and the Austrian National Bank (Jubilaumsfondsprojekt No. 16534).

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