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SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks
BACKGROUND: Recently, we developed a mathematical model for identifying putative competing endogenous RNA (ceRNA) interactions. This methodology has aroused a broad acknowledgment within the scientific community thanks to the encouraging results achieved when applied to breast invasive carcinoma, le...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9073480/ https://www.ncbi.nlm.nih.gov/pubmed/35524174 http://dx.doi.org/10.1186/s12859-022-04695-x |
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author | Paci, Paola Fiscon, Giulia |
author_facet | Paci, Paola Fiscon, Giulia |
author_sort | Paci, Paola |
collection | PubMed |
description | BACKGROUND: Recently, we developed a mathematical model for identifying putative competing endogenous RNA (ceRNA) interactions. This methodology has aroused a broad acknowledgment within the scientific community thanks to the encouraging results achieved when applied to breast invasive carcinoma, leading to the identification of PVT1, a long non-coding RNA functioning as ceRNA for the miR-200 family. The main shortcoming of the model is that it is no freely available and implemented in MATLAB®, a proprietary programming platform requiring a paid license for installing, operating, manipulating, and running the software. RESULTS: Breaking through these model limitations demands to distribute it in an open-source, freely accessible environment, such as R, designed for an ordinary audience of users that are not able to afford a proprietary solution. Here, we present SPINNAKER (SPongeINteractionNetworkmAKER), the open-source version of our widely established mathematical model for predicting ceRNAs crosstalk, that is released as an exhaustive collection of R functions. SPINNAKER has been even designed for providing many additional features that facilitate its usability, make it more efficient in terms of further implementation and extension, and less intense in terms of computational execution time. CONCLUSIONS: SPINNAKER source code is freely available at https://github.com/sportingCode/SPINNAKER.git together with a thoroughgoing PPT-based guideline. In order to help users get the key points more conveniently, also a practical R-styled plain-text guideline is provided. Finally, a short movie is available to help the user to set the own directory, properly. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-022-04695-x. |
format | Online Article Text |
id | pubmed-9073480 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-90734802022-05-06 SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks Paci, Paola Fiscon, Giulia BMC Bioinformatics Software BACKGROUND: Recently, we developed a mathematical model for identifying putative competing endogenous RNA (ceRNA) interactions. This methodology has aroused a broad acknowledgment within the scientific community thanks to the encouraging results achieved when applied to breast invasive carcinoma, leading to the identification of PVT1, a long non-coding RNA functioning as ceRNA for the miR-200 family. The main shortcoming of the model is that it is no freely available and implemented in MATLAB®, a proprietary programming platform requiring a paid license for installing, operating, manipulating, and running the software. RESULTS: Breaking through these model limitations demands to distribute it in an open-source, freely accessible environment, such as R, designed for an ordinary audience of users that are not able to afford a proprietary solution. Here, we present SPINNAKER (SPongeINteractionNetworkmAKER), the open-source version of our widely established mathematical model for predicting ceRNAs crosstalk, that is released as an exhaustive collection of R functions. SPINNAKER has been even designed for providing many additional features that facilitate its usability, make it more efficient in terms of further implementation and extension, and less intense in terms of computational execution time. CONCLUSIONS: SPINNAKER source code is freely available at https://github.com/sportingCode/SPINNAKER.git together with a thoroughgoing PPT-based guideline. In order to help users get the key points more conveniently, also a practical R-styled plain-text guideline is provided. Finally, a short movie is available to help the user to set the own directory, properly. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-022-04695-x. BioMed Central 2022-05-06 /pmc/articles/PMC9073480/ /pubmed/35524174 http://dx.doi.org/10.1186/s12859-022-04695-x Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Software Paci, Paola Fiscon, Giulia SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks |
title | SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks |
title_full | SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks |
title_fullStr | SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks |
title_full_unstemmed | SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks |
title_short | SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks |
title_sort | spinnaker: an r-based tool to highlight key rna interactions in complex biological networks |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9073480/ https://www.ncbi.nlm.nih.gov/pubmed/35524174 http://dx.doi.org/10.1186/s12859-022-04695-x |
work_keys_str_mv | AT pacipaola spinnakeranrbasedtooltohighlightkeyrnainteractionsincomplexbiologicalnetworks AT fiscongiulia spinnakeranrbasedtooltohighlightkeyrnainteractionsincomplexbiologicalnetworks |