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Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis
One of the key challenges for transcriptomics-based research is not only the processing of large data but also modeling the complexity of features that are sources of variation across samples, which is required for an accurate statistical analysis. Therefore, our goal is to foster access for wet lab...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6527599/ https://www.ncbi.nlm.nih.gov/pubmed/31139204 http://dx.doi.org/10.3389/fgene.2019.00356 |
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author | Palu, Cintia C. Ribeiro-Alves, Marcelo Wu, Yanxin Lawlor, Brendan Baranov, Pavel V. Kelly, Brian Walsh, Paul |
author_facet | Palu, Cintia C. Ribeiro-Alves, Marcelo Wu, Yanxin Lawlor, Brendan Baranov, Pavel V. Kelly, Brian Walsh, Paul |
author_sort | Palu, Cintia C. |
collection | PubMed |
description | One of the key challenges for transcriptomics-based research is not only the processing of large data but also modeling the complexity of features that are sources of variation across samples, which is required for an accurate statistical analysis. Therefore, our goal is to foster access for wet lab researchers to bioinformatics tools, in order to enhance their ability to explore biological aspects and validate hypotheses with robust analysis. In this context, user-friendly interfaces can enable researchers to apply computational biology methods without requiring bioinformatics expertise. Such bespoke platforms can improve the quality of the findings by allowing the researcher to freely explore the data and test a new hypothesis with independence. Simplicity DiffExpress is a data-driven software platform dedicated to enabling non-bioinformaticians to take ownership of the differential expression analysis (DEA) step in a transcriptomics experiment while presenting the results in a comprehensible layout, which supports an efficient results exploration, information storage, and reproducibility. Simplicity DiffExpress’ key component is the bespoke statistical model validation that guides the user through any necessary alteration in the dataset or model, tackling the challenges behind complex data analysis. The software utilizes edgeR, and it is implemented as part of the Simplicity(TM) platform, providing a dynamic interface, with well-organized results that are easy to navigate and are shareable. Computational biologists and bioinformaticians can also benefit from its use since the data validation is more informative than the usual DEA resources. Wet-lab collaborators can benefit from receiving their results in an organized interface. Simplicity DiffExpress is freely available for academic use, and it is cloud-based (https://simplicity.nsilico.com/dea). |
format | Online Article Text |
id | pubmed-6527599 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-65275992019-05-28 Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis Palu, Cintia C. Ribeiro-Alves, Marcelo Wu, Yanxin Lawlor, Brendan Baranov, Pavel V. Kelly, Brian Walsh, Paul Front Genet Genetics One of the key challenges for transcriptomics-based research is not only the processing of large data but also modeling the complexity of features that are sources of variation across samples, which is required for an accurate statistical analysis. Therefore, our goal is to foster access for wet lab researchers to bioinformatics tools, in order to enhance their ability to explore biological aspects and validate hypotheses with robust analysis. In this context, user-friendly interfaces can enable researchers to apply computational biology methods without requiring bioinformatics expertise. Such bespoke platforms can improve the quality of the findings by allowing the researcher to freely explore the data and test a new hypothesis with independence. Simplicity DiffExpress is a data-driven software platform dedicated to enabling non-bioinformaticians to take ownership of the differential expression analysis (DEA) step in a transcriptomics experiment while presenting the results in a comprehensible layout, which supports an efficient results exploration, information storage, and reproducibility. Simplicity DiffExpress’ key component is the bespoke statistical model validation that guides the user through any necessary alteration in the dataset or model, tackling the challenges behind complex data analysis. The software utilizes edgeR, and it is implemented as part of the Simplicity(TM) platform, providing a dynamic interface, with well-organized results that are easy to navigate and are shareable. Computational biologists and bioinformaticians can also benefit from its use since the data validation is more informative than the usual DEA resources. Wet-lab collaborators can benefit from receiving their results in an organized interface. Simplicity DiffExpress is freely available for academic use, and it is cloud-based (https://simplicity.nsilico.com/dea). Frontiers Media S.A. 2019-05-14 /pmc/articles/PMC6527599/ /pubmed/31139204 http://dx.doi.org/10.3389/fgene.2019.00356 Text en Copyright © 2019 Palu, Ribeiro-Alves, Wu, Lawlor, Baranov, Kelly and Walsh. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Palu, Cintia C. Ribeiro-Alves, Marcelo Wu, Yanxin Lawlor, Brendan Baranov, Pavel V. Kelly, Brian Walsh, Paul Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis |
title | Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis |
title_full | Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis |
title_fullStr | Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis |
title_full_unstemmed | Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis |
title_short | Simplicity DiffExpress: A Bespoke Cloud-Based Interface for RNA-seq Differential Expression Modeling and Analysis |
title_sort | simplicity diffexpress: a bespoke cloud-based interface for rna-seq differential expression modeling and analysis |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6527599/ https://www.ncbi.nlm.nih.gov/pubmed/31139204 http://dx.doi.org/10.3389/fgene.2019.00356 |
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