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TIminer: NGS data mining pipeline for cancer immunology and immunotherapy
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 intermed...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870678/ https://www.ncbi.nlm.nih.gov/pubmed/28633385 http://dx.doi.org/10.1093/bioinformatics/btx377 |
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author | Tappeiner, Elias Finotello, Francesca Charoentong, Pornpimol Mayer, Clemens Rieder, Dietmar Trajanoski, Zlatko |
author_facet | Tappeiner, Elias Finotello, Francesca Charoentong, Pornpimol Mayer, Clemens Rieder, Dietmar Trajanoski, Zlatko |
author_sort | Tappeiner, Elias |
collection | PubMed |
description | 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.at/software/timiner/timiner.shtml. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-5870678 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-58706782018-04-05 TIminer: NGS data mining pipeline for cancer immunology and immunotherapy Tappeiner, Elias Finotello, Francesca Charoentong, Pornpimol Mayer, Clemens Rieder, Dietmar Trajanoski, Zlatko Bioinformatics Applications Notes 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.at/software/timiner/timiner.shtml. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2017-10-01 2017-06-15 /pmc/articles/PMC5870678/ /pubmed/28633385 http://dx.doi.org/10.1093/bioinformatics/btx377 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Notes Tappeiner, Elias Finotello, Francesca Charoentong, Pornpimol Mayer, Clemens Rieder, Dietmar Trajanoski, Zlatko TIminer: NGS data mining pipeline for cancer immunology and immunotherapy |
title | TIminer: NGS data mining pipeline for cancer immunology and immunotherapy |
title_full | TIminer: NGS data mining pipeline for cancer immunology and immunotherapy |
title_fullStr | TIminer: NGS data mining pipeline for cancer immunology and immunotherapy |
title_full_unstemmed | TIminer: NGS data mining pipeline for cancer immunology and immunotherapy |
title_short | TIminer: NGS data mining pipeline for cancer immunology and immunotherapy |
title_sort | timiner: ngs data mining pipeline for cancer immunology and immunotherapy |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870678/ https://www.ncbi.nlm.nih.gov/pubmed/28633385 http://dx.doi.org/10.1093/bioinformatics/btx377 |
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