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GSA Central—A web platform to perform, learn, and discuss gene set analysis

Gene Set Analysis (GSA) is one of the most commonly used strategies to analyze omics data. Hundreds of GSA-related papers have been published, giving birth to a GSA field in Bioinformatics studies. However, as the field grows, it is becoming more difficult to obtain a clear view of all available met...

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Autores principales: Huang, Xiaowei, Lu, Xuanyi, Xie, Chengshu, Jauhari, Shaurya, Xie, Zihong, Mei, Songqing, Mora, Antonio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9403262/
https://www.ncbi.nlm.nih.gov/pubmed/36035404
http://dx.doi.org/10.3389/fmed.2022.965908
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author Huang, Xiaowei
Lu, Xuanyi
Xie, Chengshu
Jauhari, Shaurya
Xie, Zihong
Mei, Songqing
Mora, Antonio
author_facet Huang, Xiaowei
Lu, Xuanyi
Xie, Chengshu
Jauhari, Shaurya
Xie, Zihong
Mei, Songqing
Mora, Antonio
author_sort Huang, Xiaowei
collection PubMed
description Gene Set Analysis (GSA) is one of the most commonly used strategies to analyze omics data. Hundreds of GSA-related papers have been published, giving birth to a GSA field in Bioinformatics studies. However, as the field grows, it is becoming more difficult to obtain a clear view of all available methods, resources, and their quality. In this paper, we introduce a web platform called “GSA Central” which, as its name indicates, acts as a focal point to centralize GSA information and tools useful to beginners, average users, and experts in the GSA field. “GSA Central” contains five different resources: A Galaxy instance containing GSA tools (“Galaxy-GSA”), a portal to educational material (“GSA Classroom”), a comprehensive database of articles (“GSARefDB”), a set of benchmarking tools (“GSA BenchmarKING”), and a blog (“GSA Blog”). We expect that “GSA Central” will become a useful resource for users looking for introductory learning, state-of-the-art updates, method/tool selection guidelines and insights, tool usage, tool integration under a Galaxy environment, tool design, and tool validation/benchmarking. Moreover, we expect this kind of platform to become an example of a “thematic platform” containing all the resources that people in the field might need, an approach that could be extended to other bioinformatics topics or scientific fields.
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spelling pubmed-94032622022-08-26 GSA Central—A web platform to perform, learn, and discuss gene set analysis Huang, Xiaowei Lu, Xuanyi Xie, Chengshu Jauhari, Shaurya Xie, Zihong Mei, Songqing Mora, Antonio Front Med (Lausanne) Medicine Gene Set Analysis (GSA) is one of the most commonly used strategies to analyze omics data. Hundreds of GSA-related papers have been published, giving birth to a GSA field in Bioinformatics studies. However, as the field grows, it is becoming more difficult to obtain a clear view of all available methods, resources, and their quality. In this paper, we introduce a web platform called “GSA Central” which, as its name indicates, acts as a focal point to centralize GSA information and tools useful to beginners, average users, and experts in the GSA field. “GSA Central” contains five different resources: A Galaxy instance containing GSA tools (“Galaxy-GSA”), a portal to educational material (“GSA Classroom”), a comprehensive database of articles (“GSARefDB”), a set of benchmarking tools (“GSA BenchmarKING”), and a blog (“GSA Blog”). We expect that “GSA Central” will become a useful resource for users looking for introductory learning, state-of-the-art updates, method/tool selection guidelines and insights, tool usage, tool integration under a Galaxy environment, tool design, and tool validation/benchmarking. Moreover, we expect this kind of platform to become an example of a “thematic platform” containing all the resources that people in the field might need, an approach that could be extended to other bioinformatics topics or scientific fields. Frontiers Media S.A. 2022-08-11 /pmc/articles/PMC9403262/ /pubmed/36035404 http://dx.doi.org/10.3389/fmed.2022.965908 Text en Copyright © 2022 Huang, Lu, Xie, Jauhari, Xie, Mei and Mora. https://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 Medicine
Huang, Xiaowei
Lu, Xuanyi
Xie, Chengshu
Jauhari, Shaurya
Xie, Zihong
Mei, Songqing
Mora, Antonio
GSA Central—A web platform to perform, learn, and discuss gene set analysis
title GSA Central—A web platform to perform, learn, and discuss gene set analysis
title_full GSA Central—A web platform to perform, learn, and discuss gene set analysis
title_fullStr GSA Central—A web platform to perform, learn, and discuss gene set analysis
title_full_unstemmed GSA Central—A web platform to perform, learn, and discuss gene set analysis
title_short GSA Central—A web platform to perform, learn, and discuss gene set analysis
title_sort gsa central—a web platform to perform, learn, and discuss gene set analysis
topic Medicine
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9403262/
https://www.ncbi.nlm.nih.gov/pubmed/36035404
http://dx.doi.org/10.3389/fmed.2022.965908
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