STExplorer: Navigating the Micro-Geography of Spatial Omics Data
Guardat en:
| Publicat a: | bioRxiv (Jan 23, 2025) |
|---|---|
| Autor principal: | |
| Altres autors: | , , , , , , , , , , , |
| Publicat: |
Cold Spring Harbor Laboratory Press
|
| Matèries: | |
| Accés en línia: | Citation/Abstract Full Text - PDF Full text outside of ProQuest |
| Etiquetes: |
Sense etiquetes, Sigues el primer a etiquetar aquest registre!
|
MARC
| LEADER | 00000nab a2200000uu 4500 | ||
|---|---|---|---|
| 001 | 3158241612 | ||
| 003 | UK-CbPIL | ||
| 022 | |a 2692-8205 | ||
| 024 | 7 | |a 10.1101/2025.01.17.633539 |2 doi | |
| 035 | |a 3158241612 | ||
| 045 | 0 | |b d20250123 | |
| 100 | 1 | |a Zormpas, Eleftherios | |
| 245 | 1 | |a STExplorer: Navigating the Micro-Geography of Spatial Omics Data | |
| 260 | |b Cold Spring Harbor Laboratory Press |c Jan 23, 2025 | ||
| 513 | |a Working Paper | ||
| 520 | 3 | |a Spatial transcriptomics (ST) has the potential to provide unprecedented insights into gene expression across tissue architecture, but existing analytical methods often overlook the full complexity of the spatial dimension. We present STExplorer, an R package that adapts well-established computational geography (CG) methods to explore the micro-geography of spatial omics data. By incorporating techniques like Geographically Weighted Principal Component Analysis (GWPCA), Fuzzy Geographically Weighted Clustering (FGWC), Geographically Weighted Regression (GWR), and analyses of observation Spatial Autocorrelation (SA), STExplorer enables the uncovering of spatially resolved patterns that capture the spatial heterogeneity of biological data. STExplorer provides a complete suite of functions for spatial analyses and visualisations, supporting deeper biological understanding and inference. Built on the Bioconductor ecosystem, the package integrates with SpatialFeatureExperiment objects, ensuring compatibility with existing pipelines. It includes preprocessing capabilities such as data import, quality control, gene count normalisation, and variable gene selection, alongside tools for downstream analysis and detailed visualisations that quantify and map spatial heterogeneity and relationships. We demonstrate the utility of STExplorer through applications to spatial transcriptomics datasets, revealing that spatially varying gene expression and relationships are often masked by standard analyses. By bridging bioinformatics and CG, STExplorer provides a novel and informed approach to spatial transcriptomics analysis, with robust tools to address spatial heterogeneity and its associated underlying biology, thereby advancing our understanding of complex tissue biology without reinventing the wheel.Competing Interest StatementThe authors have declared no competing interest.Footnotes* Page margins changed so bioRxiv header does not overlap text; no alterations to content.* https://github.com/LefterisZ/STExplorer* https://github.com/ncl-icbam/STExplorer_Analysis | |
| 653 | |a Data processing | ||
| 653 | |a Gene expression | ||
| 653 | |a Transcriptomics | ||
| 653 | |a Quality control | ||
| 653 | |a Principal components analysis | ||
| 653 | |a Bioinformatics | ||
| 653 | |a Geography | ||
| 653 | |a Spatial heterogeneity | ||
| 700 | 1 | |a Vlachogiannis, Nikolaos I | |
| 700 | 1 | |a Resteu, Anastasia | |
| 700 | 1 | |a Unsworth, Adrienne | |
| 700 | 1 | |a Simon Tual-Chalot | |
| 700 | 1 | |a Dorgau, Birthe | |
| 700 | 1 | |a Queen, Rachel | |
| 700 | 1 | |a Lako, Majlinda | |
| 700 | 1 | |a Tiniakos, Dina | |
| 700 | 1 | |a Comber, Alexis | |
| 700 | 1 | |a Anstee, Quentin M | |
| 700 | 1 | |a Giakountis, Antonis | |
| 700 | 1 | |a Cockell, Simon J | |
| 773 | 0 | |t bioRxiv |g (Jan 23, 2025) | |
| 786 | 0 | |d ProQuest |t Biological Science Database | |
| 856 | 4 | 1 | |3 Citation/Abstract |u https://www.proquest.com/docview/3158241612/abstract/embedded/L8HZQI7Z43R0LA5T?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text - PDF |u https://www.proquest.com/docview/3158241612/fulltextPDF/embedded/L8HZQI7Z43R0LA5T?source=fedsrch |
| 856 | 4 | 0 | |3 Full text outside of ProQuest |u https://www.biorxiv.org/content/10.1101/2025.01.17.633539v2 |