{"id":32111292,"url":"https://github.com/jefworks-lab/seraster","last_synced_at":"2026-02-18T20:31:45.677Z","repository":{"id":218110545,"uuid":"682123112","full_name":"JEFworks-Lab/SEraster","owner":"JEFworks-Lab","description":"Spatial Experiments raster - a rasterization preprocessing framework for scalable spatial omics data analysis","archived":false,"fork":false,"pushed_at":"2025-04-23T01:53:26.000Z","size":45978,"stargazers_count":19,"open_issues_count":1,"forks_count":5,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-01-26T22:22:57.117Z","etag":null,"topics":["rstats","spatial-analysis","spatial-data-analysis","spatial-omics","spatial-transcriptomics"],"latest_commit_sha":null,"homepage":"https://jef.works/SEraster/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/JEFworks-Lab.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2023-08-23T13:45:37.000Z","updated_at":"2025-12-12T16:03:52.000Z","dependencies_parsed_at":"2024-02-20T20:45:22.490Z","dependency_job_id":"f7c70099-9e3a-49cf-ace9-1d8692f213d4","html_url":"https://github.com/JEFworks-Lab/SEraster","commit_stats":{"total_commits":50,"total_committers":4,"mean_commits":12.5,"dds":0.28,"last_synced_commit":"676af113625a441d9f0dc524faed0a474ea193b7"},"previous_names":["jefworks-lab/seraster"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/JEFworks-Lab/SEraster","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JEFworks-Lab%2FSEraster","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JEFworks-Lab%2FSEraster/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JEFworks-Lab%2FSEraster/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JEFworks-Lab%2FSEraster/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JEFworks-Lab","download_url":"https://codeload.github.com/JEFworks-Lab/SEraster/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JEFworks-Lab%2FSEraster/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29594259,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-18T18:54:29.675Z","status":"ssl_error","status_checked_at":"2026-02-18T18:50:50.517Z","response_time":162,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["rstats","spatial-analysis","spatial-data-analysis","spatial-omics","spatial-transcriptomics"],"created_at":"2025-10-20T14:23:03.059Z","updated_at":"2026-02-18T20:31:45.669Z","avatar_url":"https://github.com/JEFworks-Lab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Spatial Experiments raster (SEraster)\n\n`SEraster` is a rasterization preprocessing framework that aggregates cellular information into spatial pixels to reduce resource requirements for spatial omics data analysis. This is the `SEraster` R documentation website. Questions, suggestions, or problems should be submitted as [GitHub issues](https://github.com/JEFworks-Lab/SEraster/issues).\n\n\u003cp\u003e\n\n\u003cimg src=\"https://github.com/JEFworks/SEraster/blob/main/images/seraster_logo_hex.png?raw=true\" align=\"center\" height=\"300\" style=\"float: center; height:300px;\"/\u003e\n\n\u003c/p\u003e\n\n## Overview\n\n`SEraster` reduces the number of spatial points in spatial omics datasets for downstream analysis through a process of rasterization where single cells' gene expression or cell-type labels are aggregated into equally sized pixels based on a user-defined `resolution`. Here, we refer to a particular `resolution` of rasterization by the side length of the pixel such that finer `resolution` indicates smaller pixel size and coarser `resolution` indicates larger pixel size.\n\n\u003cp align=\"center\"\u003e\n\n\u003cimg src=\"https://github.com/JEFworks-Lab/SEraster/blob/main/images/overview.png?raw=true\" height=\"600\"/\u003e\n\n\u003c/p\u003e\n\n## Installation\n\nTo install `SEraster` using Bioconductor, start R (version \"4.5.0\") and run:\n\n```r\nif (!require(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(\"SEraster\")\n```\n\n[See Bioconductor for more details](https://bioconductor.org/packages/release/bioc/html/SEraster.html).\n\nThe latest development version can also be installed from [GitHub](https://github.com/JEFworks-Lab/SEraster) using `remotes`:\n\n```r\nrequire(remotes)\nremotes::install_github('JEFworks-Lab/SEraster')\n```\n\nIn addition, `SEraster` is also compatible with `SeuratObject` through `SeuratWrappers`. `SeuratWrappers` implementation can be installed using `remotes`:\n\n```r\nrequire(remotes)\nremotes::install_github('satijalab/seurat-wrappers@SEraster')\n```\n\nDocumentation and tutorial for the `SeuratWrappers` implementation can be found in the `SEraster` branch of the [`SeuratWrappers` GitHub repository](https://github.com/satijalab/seurat-wrappers/tree/SEraster).\n\n## Tutorials\n\nIntroduction:\n\n-   [Formatting a SpatialExperiment Object for SEraster](https://jef.works/SEraster/articles/formatting-SpatialExperiment-for-SEraster.html)\n-   [Getting Started With SEraster](https://jef.works/SEraster/articles/getting-started-with-SEraster.html)\n-   [SEraster for Spatial Variable Genes Analysis](https://jef.works/SEraster/articles/SEraster-for-SVG-analysis.html)\n-   [Characterizing mPOA cell-type heterogeneity with spatial bootstrapping](https://jef.works/SEraster/articles/characterizing-mPOA-cell-type-heterogeneity.html)\n\n## Citation\n\nOur manuscript describing `SEraster` is available on *Bioinformatics*:\n\n[Gohta Aihara, Kalen Clifton, Mayling Chen, Zhuoyan Li, Lyla Atta, Brendan F Miller, Rahul Satija, John W Hickey, Jean Fan, SEraster: a rasterization preprocessing framework for scalable spatial omics data analysis, Bioinformatics, Volume 40, Issue 7, July 2024, btae412, https://doi.org/10.1093/bioinformatics/btae412](https://academic.oup.com/bioinformatics/article/40/7/btae412/7696710)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjefworks-lab%2Fseraster","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjefworks-lab%2Fseraster","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjefworks-lab%2Fseraster/lists"}