{"id":22021751,"url":"https://github.com/lieberinstitute/visiumstitched","last_synced_at":"2025-03-23T10:21:00.985Z","repository":{"id":203347230,"uuid":"709323164","full_name":"LieberInstitute/visiumStitched","owner":"LieberInstitute","description":"R package containing functions useful for stitching Visium capture areas. 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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# visiumStitched \u003cimg src=\"man/figures/logo.png\" align=\"right\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![DOI](https://zenodo.org/badge/709323164.svg)](https://zenodo.org/doi/10.5281/zenodo.13012339)\n[![GitHub issues](https://img.shields.io/github/issues/LieberInstitute/visiumStitched)](https://github.com/LieberInstitute/visiumStitched/issues)\n[![GitHub pulls](https://img.shields.io/github/issues-pr/LieberInstitute/visiumStitched)](https://github.com/LieberInstitute/visiumStitched/pulls)\n[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)\n[![check-bioc](https://github.com/LieberInstitute/visiumStitched/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/LieberInstitute/visiumStitched/actions/workflows/check-bioc.yml)\n[![Codecov test coverage](https://codecov.io/gh/LieberInstitute/visiumStitched/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/LieberInstitute/visiumStitched?branch=devel)\n[![Bioc release status](http://www.bioconductor.org/shields/build/release/bioc/visiumStitched.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/visiumStitched)\n[![Bioc devel status](http://www.bioconductor.org/shields/build/devel/bioc/visiumStitched.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/visiumStitched)\n[![Bioc downloads rank](https://bioconductor.org/shields/downloads/release/visiumStitched.svg)](http://bioconductor.org/packages/stats/bioc/visiumStitched/)\n[![Bioc support](https://bioconductor.org/shields/posts/visiumStitched.svg)](https://support.bioconductor.org/tag/visiumStitched)\n[![Bioc history](https://bioconductor.org/shields/years-in-bioc/visiumStitched.svg)](https://bioconductor.org/packages/release/bioc/html/visiumStitched.html#since)\n[![Bioc last commit](https://bioconductor.org/shields/lastcommit/devel/bioc/visiumStitched.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/visiumStitched/)\n[![Bioc dependencies](https://bioconductor.org/shields/dependencies/release/visiumStitched.svg)](https://bioconductor.org/packages/release/bioc/html/visiumStitched.html#since)\n\u003c!-- badges: end --\u003e\n\n`visiumStitched` provides helper functions for working with\tmultiple Visium\ncapture areas that overlap each other. This package was developed along with\nthe companion example use case data available from\nhttps://github.com/LieberInstitute/visiumStitched_brain. `visiumStitched`\nprepares `SpaceRanger` (10x Genomics) output files so you can stitch the images\nfrom groups of capture areas together with `Fiji`. Then `visiumStitched` builds\na `SpatialExperiment` object with the stitched data and makes an artificial\nhexagonal grid enabling the seamless use of spatial clustering methods that rely\non such grid to identify neighboring spots, such as `PRECAST` and `BayesSpace`.\nThe `SpatialExperiment` objects created by `visiumStitched` are compatible with\n`spatialLIBD`, which can be used to build interactive websites for stitched\n`SpatialExperiment` objects (check the\n[example human brain data](https://libd.shinyapps.io/visiumStitched_brain)).\n`visiumStitched` also enables casting `SpatialExperiment` objects as `Seurat`\nobjects.\n\nFor details, check the\n[documentation site](http://research.libd.org/visiumStitched/).\n\n## Example data processed with visiumStitched\n\nHere is example human brain data from\n[LieberInstitute/visiumStitched_brain](https://github.com/LieberInstitute/visiumStitched_brain)\nthat was stitched together using `visiumStitched`. The resulting data can be\naccessed and visualized with\n[`spatialLIBD`](https://research.libd.org/spatialLIBD/) version 1.17.8 or newer.\n\n```{r \"example_visiumStitched_brain\"}\n## Check that you have a recent version of spatialLIBD installed\nstopifnot(packageVersion(\"spatialLIBD\") \u003e= \"1.17.8\")\n\n## Download the spot-level data, which is a SpatialExperiment object\nspe \u003c- spatialLIBD::fetch_data(type = \"visiumStitched_brain_spe\")\n\n## Explore the stitched data\nspe\n\n## Show clustering results from PRECAST at k = 8\nspatialLIBD::vis_clus(\n    spe,\n    clustervar = \"precast_k8_stitched\",\n    is_stitched = TRUE\n)\n```\n\n\n## Installation instructions\n\nGet the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then\ninstall `visiumStitched` from Bioconductor using the following code:\n\n```{r 'install', eval = FALSE}\nif (!requireNamespace(\"BiocManager\", quietly = TRUE)) {\n    install.packages(\"BiocManager\")\n}\n\nBiocManager::install(\"visiumStitched\")\n```\n\n## Citation\n\nBelow is the citation output from using `citation('visiumStitched')` in R.\nPlease run this yourself to check for any updates on how to cite\n__visiumStitched__.\n\n```{r 'citation', eval = requireNamespace('visiumStitched')}\nprint(citation(\"visiumStitched\"), bibtex = TRUE)\n```\n\nPlease note that the `visiumStitched` was only made possible thanks to many\nother R and bioinformatics software authors, which are cited either in the\nvignettes and/or the paper(s) describing this package.\n\n## Code of Conduct\n\nPlease note that the `visiumStitched` project is released with a\n[Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/).\nBy contributing to this project, you agree to abide by its terms.\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 `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.\n* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.\n* The [documentation website](http://LieberInstitute.github.io/visiumStitched) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.\n* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.\n* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.\n\nFor more details, check the `dev` directory.\n\nThis package was developed using `r BiocStyle::Biocpkg('biocthis')`.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flieberinstitute%2Fvisiumstitched","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flieberinstitute%2Fvisiumstitched","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flieberinstitute%2Fvisiumstitched/lists"}