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MetaMutationalSigs: comparison of mutational signature refitting results made easy
MOTIVATION: The analysis of mutational signatures is becoming increasingly common in cancer genetics, with emerging implications in cancer evolution, classification, treatment decision and prognosis. Recently, several packages have been developed for mutational signature analysis, with each using di...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9004636/ https://www.ncbi.nlm.nih.gov/pubmed/35157026 http://dx.doi.org/10.1093/bioinformatics/btac091 |
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author | Pandey, Palash Arora, Sanjeevani Rosen, Gail L |
author_facet | Pandey, Palash Arora, Sanjeevani Rosen, Gail L |
author_sort | Pandey, Palash |
collection | PubMed |
description | MOTIVATION: The analysis of mutational signatures is becoming increasingly common in cancer genetics, with emerging implications in cancer evolution, classification, treatment decision and prognosis. Recently, several packages have been developed for mutational signature analysis, with each using different methodology and yielding significantly different results. Because of the non-trivial differences in tools’ refitting results, researchers may desire to survey and compare the available tools, in order to objectively evaluate the results for their specific research question, such as which mutational signatures are prevalent in different cancer types. RESULTS: Due to the need for effective comparison of refitting mutational signatures, we introduce a user-friendly software that can aggregate and visually present results from different refitting packages. AVAILABILITY AND IMPLEMENTATION: MetaMutationalSigs is implemented using R and python and is available for installation using Docker and available at: https://github.com/EESI/MetaMutationalSigs. |
format | Online Article Text |
id | pubmed-9004636 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-90046362022-04-13 MetaMutationalSigs: comparison of mutational signature refitting results made easy Pandey, Palash Arora, Sanjeevani Rosen, Gail L Bioinformatics Applications Note MOTIVATION: The analysis of mutational signatures is becoming increasingly common in cancer genetics, with emerging implications in cancer evolution, classification, treatment decision and prognosis. Recently, several packages have been developed for mutational signature analysis, with each using different methodology and yielding significantly different results. Because of the non-trivial differences in tools’ refitting results, researchers may desire to survey and compare the available tools, in order to objectively evaluate the results for their specific research question, such as which mutational signatures are prevalent in different cancer types. RESULTS: Due to the need for effective comparison of refitting mutational signatures, we introduce a user-friendly software that can aggregate and visually present results from different refitting packages. AVAILABILITY AND IMPLEMENTATION: MetaMutationalSigs is implemented using R and python and is available for installation using Docker and available at: https://github.com/EESI/MetaMutationalSigs. Oxford University Press 2022-02-14 /pmc/articles/PMC9004636/ /pubmed/35157026 http://dx.doi.org/10.1093/bioinformatics/btac091 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Applications Note Pandey, Palash Arora, Sanjeevani Rosen, Gail L MetaMutationalSigs: comparison of mutational signature refitting results made easy |
title | MetaMutationalSigs: comparison of mutational signature refitting results made easy |
title_full | MetaMutationalSigs: comparison of mutational signature refitting results made easy |
title_fullStr | MetaMutationalSigs: comparison of mutational signature refitting results made easy |
title_full_unstemmed | MetaMutationalSigs: comparison of mutational signature refitting results made easy |
title_short | MetaMutationalSigs: comparison of mutational signature refitting results made easy |
title_sort | metamutationalsigs: comparison of mutational signature refitting results made easy |
topic | Applications Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9004636/ https://www.ncbi.nlm.nih.gov/pubmed/35157026 http://dx.doi.org/10.1093/bioinformatics/btac091 |
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