Kariotis, S. orcid.org/0000-0001-9993-6017, Tan, P.F. orcid.org/0000-0003-1475-8886, Lu, H. orcid.org/0000-0002-0349-2181 et al. (4 more authors) (2024) Omada: robust clustering of transcriptomes through multiple testing. GigaScience, 13 (2024). giae039. ISSN 2047-217X
Abstract
Background
Cohort studies increasingly collect biosamples for molecular profiling and are observing molecular heterogeneity. High-throughput RNA sequencing is providing large datasets capable of reflecting disease mechanisms. Clustering approaches have produced a number of tools to help dissect complex heterogeneous datasets, but selecting the appropriate method and parameters to perform exploratory clustering analysis of transcriptomic data requires deep understanding of machine learning and extensive computational experimentation. Tools that assist with such decisions without prior field knowledge are nonexistent. To address this, we have developed Omada, a suite of tools aiming to automate these processes and make robust unsupervised clustering of transcriptomic data more accessible through automated machine learning–based functions.
Findings
The efficiency of each tool was tested with 7 datasets characterized by different expression signal strengths to capture a wide spectrum of RNA expression datasets. Our toolkit’s decisions reflected the real number of stable partitions in datasets where the subgroups are discernible. Within datasets with less clear biological distinctions, our tools either formed stable subgroups with different expression profiles and robust clinical associations or revealed signs of problematic data such as biased measurements.
Conclusions
In conclusion, Omada successfully automates the robust unsupervised clustering of transcriptomic data, making advanced analysis accessible and reliable even for those without extensive machine learning expertise. Implementation of Omada is available at http://bioconductor.org/packages/omada/.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © The Author(s) 2024. Published by Oxford University Press GigaScience. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/ ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
Keywords: | unsupervised learning; cluster analysis; gene expression; software toolkit |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Engineering (Sheffield) > Department of Computer Science (Sheffield) |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 17 Jul 2024 08:17 |
Last Modified: | 22 Jul 2024 11:05 |
Status: | Published |
Publisher: | Oxford University Press (OUP) |
Refereed: | Yes |
Identification Number: | 10.1093/gigascience/giae039 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:214815 |