Protocol to boost the robustness and accuracy of spatial transcriptomics algorithms using ensemble techniques
Summary: Spatial transcriptomics enhances our understanding of cellular organization by mapping gene expression data to precise tissue locations. Here, we present a protocol for using weighted ensemble method for spatial transcriptomics (WEST), which uses ensemble techniques to boost the robustness...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-03-01
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| Series: | STAR Protocols |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166725000140 |
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| author | Jiazhang Cai Shushan Wu Huimin Cheng Wenxuan Zhong Guo-Cheng Yuan Ping Ma |
| author_facet | Jiazhang Cai Shushan Wu Huimin Cheng Wenxuan Zhong Guo-Cheng Yuan Ping Ma |
| author_sort | Jiazhang Cai |
| collection | DOAJ |
| description | Summary: Spatial transcriptomics enhances our understanding of cellular organization by mapping gene expression data to precise tissue locations. Here, we present a protocol for using weighted ensemble method for spatial transcriptomics (WEST), which uses ensemble techniques to boost the robustness and accuracy of existing algorithms. We describe steps for preprocessing data, obtaining embeddings from individual algorithms, and ensemble integrating all embeddings as a similarity matrix. We then detail procedures for using the similarity matrix to identify spatial domains and obtain new embeddings.For complete details on the use and execution of this protocol, please refer to Cai et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-cd505aed6ad045ab8d640b55bdb32994 |
| institution | Kabale University |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-cd505aed6ad045ab8d640b55bdb329942025-01-29T05:02:00ZengElsevierSTAR Protocols2666-16672025-03-0161103608Protocol to boost the robustness and accuracy of spatial transcriptomics algorithms using ensemble techniquesJiazhang Cai0Shushan Wu1Huimin Cheng2Wenxuan Zhong3Guo-Cheng Yuan4Ping Ma5Department of Statistics, University of Georgia, 310 Herty Drive, Athens, GA 30602, USADepartment of Statistics, University of Georgia, 310 Herty Drive, Athens, GA 30602, USADepartment of Biostatistics, Boston University, 801 Massachusetts Avenue Crosstown Center, Boston, MA 02118, USADepartment of Statistics, University of Georgia, 310 Herty Drive, Athens, GA 30602, USA; Corresponding authorDepartment of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY 10029, USA; Corresponding authorDepartment of Statistics, University of Georgia, 310 Herty Drive, Athens, GA 30602, USA; Corresponding authorSummary: Spatial transcriptomics enhances our understanding of cellular organization by mapping gene expression data to precise tissue locations. Here, we present a protocol for using weighted ensemble method for spatial transcriptomics (WEST), which uses ensemble techniques to boost the robustness and accuracy of existing algorithms. We describe steps for preprocessing data, obtaining embeddings from individual algorithms, and ensemble integrating all embeddings as a similarity matrix. We then detail procedures for using the similarity matrix to identify spatial domains and obtain new embeddings.For complete details on the use and execution of this protocol, please refer to Cai et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166725000140bioinformaticsgenomicsRNA-seqcomputer sciences |
| spellingShingle | Jiazhang Cai Shushan Wu Huimin Cheng Wenxuan Zhong Guo-Cheng Yuan Ping Ma Protocol to boost the robustness and accuracy of spatial transcriptomics algorithms using ensemble techniques STAR Protocols bioinformatics genomics RNA-seq computer sciences |
| title | Protocol to boost the robustness and accuracy of spatial transcriptomics algorithms using ensemble techniques |
| title_full | Protocol to boost the robustness and accuracy of spatial transcriptomics algorithms using ensemble techniques |
| title_fullStr | Protocol to boost the robustness and accuracy of spatial transcriptomics algorithms using ensemble techniques |
| title_full_unstemmed | Protocol to boost the robustness and accuracy of spatial transcriptomics algorithms using ensemble techniques |
| title_short | Protocol to boost the robustness and accuracy of spatial transcriptomics algorithms using ensemble techniques |
| title_sort | protocol to boost the robustness and accuracy of spatial transcriptomics algorithms using ensemble techniques |
| topic | bioinformatics genomics RNA-seq computer sciences |
| url | http://www.sciencedirect.com/science/article/pii/S2666166725000140 |
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