{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/scgist-gene-panel-design-for-spatial","title":"scGIST: gene panel design for spatial transcriptomics with prioritized gene sets","arxiv_id":null,"date":"2024-02-26","proceeding":"Genome Biology 2024 2","authors":["Mashrur Ahmed Yafi","Md. Hasibul Husain Hisham","Francisco Grisanti","James F. Martin","Atif Rahman","Md. Abul Hassan Samee"],"abstract":"A critical challenge of single-cell spatial transcriptomics (sc-ST) technologies is their panel size. Being based on fluorescence in situ hybridization, they are typically limited to panels of about a thousand genes. This constrains researchers to build panels from only the marker genes of different cell types and forgo other genes of interest, e.g., genes encoding ligand-receptor complexes or those in specific pathways. We propose scGIST, a constrained feature selection tool that designs sc-ST panels prioritizing user-specified genes without compromising cell type detection accuracy. We demonstrate scGIST’s efficacy in diverse use cases, highlighting it as a valuable addition to sc-ST’s algorithmic toolbox.","url_abs":"https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03185-y","url_pdf":"https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03185-y","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"scgist-gene-panel-design-for-spatial","repo_url":"https://github.com/yafi38/scGIST","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"tf","reach":null}],"tasks":[{"task_slug":"feature-selection","task_name":"feature selection"}],"methods":[{"method_slug":"feature-selection","method_name":"Feature Selection"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}