{"id":24759185,"url":"https://github.com/mictott/spotsweeper","last_synced_at":"2025-10-11T06:31:30.187Z","repository":{"id":222393547,"uuid":"712110904","full_name":"MicTott/SpotSweeper","owner":"MicTott","description":"Spatially-aware quality control for spatial transcriptomics","archived":false,"fork":false,"pushed_at":"2025-09-12T16:12:47.000Z","size":48723,"stargazers_count":12,"open_issues_count":6,"forks_count":1,"subscribers_count":4,"default_branch":"devel","last_synced_at":"2025-09-24T11:55:23.121Z","etag":null,"topics":["bioconductor","quality-control","spatial-transcriptomics"],"latest_commit_sha":null,"homepage":"https://mictott.github.io/SpotSweeper/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MicTott.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":".github/SUPPORT.md","governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-10-30T20:12:02.000Z","updated_at":"2025-09-12T16:06:22.000Z","dependencies_parsed_at":"2024-02-14T00:24:50.117Z","dependency_job_id":"62b72590-eab7-4683-b4e5-83d6de759f58","html_url":"https://github.com/MicTott/SpotSweeper","commit_stats":null,"previous_names":["mictott/spotsweeper"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/MicTott/SpotSweeper","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MicTott%2FSpotSweeper","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MicTott%2FSpotSweeper/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MicTott%2FSpotSweeper/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MicTott%2FSpotSweeper/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MicTott","download_url":"https://codeload.github.com/MicTott/SpotSweeper/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MicTott%2FSpotSweeper/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279006456,"owners_count":26084108,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-11T02:00:06.511Z","response_time":55,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":["bioconductor","quality-control","spatial-transcriptomics"],"created_at":"2025-01-28T16:51:06.191Z","updated_at":"2025-10-11T06:31:29.612Z","avatar_url":"https://github.com/MicTott.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n    collapse = TRUE,\n    comment = \"#\u003e\",\n    fig.path = \"man/figures/README-\",\n    out.width = \"100%\"\n)\n```\n\n# SpotSweeper \u003cimg src=\"man/figures/hexsticker.png\" align=\"right\" style=\"width:200px;\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)\n[![codecov](https://codecov.io/gh/MicTott/SpotSweeper/graph/badge.svg?token=M1MUJN7VS6)](https://codecov.io/gh/MicTott/SpotSweeper)\n\u003c!-- badges: end --\u003e\n\n`SpotSweeper` is a package developed for spatially-aware quality control (QC) methods for the detection, visualization, and removal of both local outliers and regional artifacts in spot-based spatial transcriptomics data, such as 10x Genomics `Visium`, using standard QC metrics. \n\nIf you experience any issues using the package or would like to make a suggestuin, please open an issue on the [GitHub repository](https://github.com/MicTott/SpotSweeper/issues).\n\nTo find more information, please visit the [documentation website](http://MicTott.github.io/SpotSweeper).\n\n```{r schematic, echo=FALSE, out.width = '100%'}\nknitr::include_graphics(\"./man/figures/schematic.png\")\n```\n\n\n## Installation instructions\n\nYou can install the latest version of `SpotSweeper` from Bioconductor with the following code: \n```{r 'install', eval = FALSE}\nif (!requireNamespace(\"BiocManager\", quietly = TRUE)) {\n    install.packages(\"BiocManager\")\n}\n\nBiocManager::install(\"SpotSweeper\")\n```\n\nThe latest development version can be installed from [GitHub](https://github.com/MicTott/SpotSweeper) using the following: \n\n```{r 'install_dev', eval = FALSE}\nif (!require(\"devtools\")) install.packages(\"devtools\")\nremotes::install_github(\"MicTott/SpotSweeper\")\n```\n\n## Tutorials\n\nA detailed tutorial is available in the package vignette from Bioconductor. A direct link to the tutorial / package vignette is available [here](https://mictott.github.io/SpotSweeper/articles/getting_started.html).\n\n\n## Development tools\n\n- Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)  through `BiocStyle::Biocpkg('biocthis')`.\n-  The [documentation website](http://MicTott.github.io/SpotSweeper) is automatically updated thanks to `BiocStyle::CRANpkg('pkgdown')`.\n-  The code is styled automatically thanks to `BiocStyle::CRANpkg('styler')`.\n-  The documentation is formatted thanks to `BiocStyle::CRANpkg('devtools')` and `BiocStyle::CRANpkg('roxygen2')`.\n\nThis package was developed using `BiocStyle::Biocpkg('biocthis')`.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmictott%2Fspotsweeper","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmictott%2Fspotsweeper","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmictott%2Fspotsweeper/lists"}