{"id":27879081,"url":"https://github.com/sales-lab/spatialde","last_synced_at":"2025-05-05T03:18:02.911Z","repository":{"id":47182205,"uuid":"322573589","full_name":"sales-lab/spatialDE","owner":"sales-lab","description":"R wrapper for SpatialDE","archived":false,"fork":false,"pushed_at":"2025-04-16T06:27:37.000Z","size":1538,"stargazers_count":3,"open_issues_count":0,"forks_count":3,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-05-05T03:17:57.608Z","etag":null,"topics":["python","r","spatial-data","transcriptomics","wrapper"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sales-lab.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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}},"created_at":"2020-12-18T11:18:55.000Z","updated_at":"2025-04-15T12:59:38.000Z","dependencies_parsed_at":"2025-04-15T13:37:37.593Z","dependency_job_id":null,"html_url":"https://github.com/sales-lab/spatialDE","commit_stats":{"total_commits":235,"total_committers":8,"mean_commits":29.375,"dds":0.5446808510638298,"last_synced_commit":"6b99d2906dec0da0fae5314c5fad31ac3f371e75"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sales-lab%2FspatialDE","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sales-lab%2FspatialDE/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sales-lab%2FspatialDE/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sales-lab%2FspatialDE/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sales-lab","download_url":"https://codeload.github.com/sales-lab/spatialDE/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":252429954,"owners_count":21746574,"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","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":["python","r","spatial-data","transcriptomics","wrapper"],"created_at":"2025-05-05T03:18:02.254Z","updated_at":"2025-05-05T03:18:02.899Z","avatar_url":"https://github.com/sales-lab.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# spatialDE\n\n\u003c!-- badges: start --\u003e\n[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)\n[![R-CMD-check-bioc](https://github.com/sales-lab/spatialDE/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/sales-lab/spatialDE/actions)\n[![Codecov test coverage](https://codecov.io/gh/sales-lab/spatialDE/branch/main/graph/badge.svg)](https://codecov.io/gh/sales-lab/spatialDE?branch=main)\n[![BioC release status](http://www.bioconductor.org/shields/build/release/bioc/spatialDE.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/spatialDE)\n[![BioC devel status](http://www.bioconductor.org/shields/build/devel/bioc/spatialDE.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/spatialDE)\n\u003c!-- badges: end --\u003e\n\nThe **spatialDE** package provides an R wrapper for the Python SpatialDE library,\nusing `r BiocStyle::CRANpkg(\"reticulate\")` and `r BiocStyle::Biocpkg(\"basilisk\")`.\n\n[SpatialDE](https://github.com/Teichlab/SpatialDE), by [Svensson et al., 2018][Svensson2018],\nis a method to identify spatially variable genes (SVGs) in spatially resolved transcriptomics data.\n\nThis package started as part of the\n[BiocSpatialChallenges](https://helenalc.github.io/BiocSpatialChallenges/index.html).\n\n\n## Installation instructions\n\nGet the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then\ninstall `r BiocStyle::Biocpkg(\"spatialDE\")` from\n[*Bioconductor*](http://bioconductor.org/) using the following code:\n\n```{r 'install', eval = FALSE}\nif (!requireNamespace(\"BiocManager\", quietly = TRUE)) {\n    install.packages(\"BiocManager\")\n}\n\nBiocManager::install(\"spatialDE\")\n```\n\nThe development version of **spatialDE** can be installed from\n[GitHub](https://github.com/sales-lab/spatialDE) with:\n\n```{r 'install_dev', eval = FALSE}\nif (!requireNamespace(\"BiocManager\", quietly = TRUE)) {\n    install.packages(\"BiocManager\")\n    \nBiocManager::install(\"sales-lab/spatialDE\")\n```\n\n\n## Basic usage\n\n```{r usage, eval=TRUE}\nlibrary(spatialDE)\nspe \u003c- mockSVG(return_SPE = TRUE)\nde_results \u003c- spatialDE(spe)\nhead(de_results)\n```\n\n\n## Citation\n\nBelow is the citation output from using `citation('spatialDE')` in R. Please\nrun this yourself to check for any updates on how to cite __spatialDE__.\n\nPlease note that this package merely provides a wrapper to use the original Python methods in R. If you find these methods useful, please also consider citing the [original paper][Svensson2018].\n\n```{r 'citation', eval = requireNamespace('spatialDE'), echo = FALSE, comment = \"\"}\nprint(citation('spatialDE'), bibtex = TRUE)\n```\n\n\n## Code of Conduct\n\nPlease note that the **spatialDE** project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.\n\n\n## Useful links\n\n- `r BiocStyle::Biocpkg(\"SpatialExperiment\")`\n- [BiocSpatialChallenges](https://helenalc.github.io/BiocSpatialChallenges/index.html)\n\nThis package was developed using `r BiocStyle::Biocpkg('biocthis')`.\n\n[Svensson2018]: https://doi.org/10.1038/nmeth.4636\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsales-lab%2Fspatialde","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsales-lab%2Fspatialde","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsales-lab%2Fspatialde/lists"}