{"id":14967209,"url":"https://github.com/lieberinstitute/spatiallibd","last_synced_at":"2025-10-06T16:03:02.040Z","repository":{"id":37772479,"uuid":"225913568","full_name":"LieberInstitute/spatialLIBD","owner":"LieberInstitute","description":"Code for the spatialLIBD R/Bioconductor package and shiny app","archived":false,"fork":false,"pushed_at":"2025-09-26T14:23:18.000Z","size":301146,"stargazers_count":96,"open_issues_count":24,"forks_count":23,"subscribers_count":19,"default_branch":"devel","last_synced_at":"2025-09-26T15:29:00.007Z","etag":null,"topics":["10xgenomics","bioconductor","golem","rstats","shiny","spatial-transcriptomics","spatialexperiment","spatiallibd","visium"],"latest_commit_sha":null,"homepage":"http://LieberInstitute.github.io/spatialLIBD/","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/LieberInstitute.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":null,"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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2019-12-04T16:46:09.000Z","updated_at":"2025-09-26T13:40:11.000Z","dependencies_parsed_at":"2024-02-19T21:30:45.704Z","dependency_job_id":"463ea367-65b1-45ab-9016-25ad69b88a13","html_url":"https://github.com/LieberInstitute/spatialLIBD","commit_stats":{"total_commits":699,"total_committers":11,"mean_commits":63.54545454545455,"dds":0.2174535050071531,"last_synced_commit":"a87428b7675532ed6e38baba05be500b943389a8"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/LieberInstitute/spatialLIBD","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2FspatialLIBD","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2FspatialLIBD/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2FspatialLIBD/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2FspatialLIBD/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LieberInstitute","download_url":"https://codeload.github.com/LieberInstitute/spatialLIBD/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LieberInstitute%2FspatialLIBD/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278638111,"owners_count":26019943,"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":"2025-10-06T02:00:05.630Z","response_time":65,"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":["10xgenomics","bioconductor","golem","rstats","shiny","spatial-transcriptomics","spatialexperiment","spatiallibd","visium"],"created_at":"2024-09-24T13:37:38.516Z","updated_at":"2025-10-06T16:03:02.002Z","avatar_url":"https://github.com/LieberInstitute.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# spatialLIBD \u003cimg src=\"man/figures/logo.png\" align=\"right\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)\n[![Bioc release status](http://www.bioconductor.org/shields/build/release/data-experiment/spatialLIBD.svg)](https://bioconductor.org/checkResults/release/data-experiment-LATEST/spatialLIBD)\n[![Bioc devel status](http://www.bioconductor.org/shields/build/devel/data-experiment/spatialLIBD.svg)](https://bioconductor.org/checkResults/devel/data-experiment-LATEST/spatialLIBD)\n[![Bioc downloads rank](https://bioconductor.org/shields/downloads/release/spatialLIBD.svg)](http://bioconductor.org/packages/stats/bioc/spatialLIBD/)\n[![Bioc support](https://bioconductor.org/shields/posts/spatialLIBD.svg)](https://support.bioconductor.org/tag/spatialLIBD)\n[![Bioc last commit](https://bioconductor.org/shields/lastcommit/devel/data-experiment/spatialLIBD.svg)](http://bioconductor.org/checkResults/devel/data-experiment-LATEST/spatialLIBD/)\n[![Bioc dependencies](https://bioconductor.org/shields/dependencies/release/spatialLIBD.svg)](https://bioconductor.org/packages/release/data-experiment/html/spatialLIBD.html#since)\n[![Codecov test coverage](https://codecov.io/gh/LieberInstitute/spatialLIBD/branch/devel/graph/badge.svg)](https://codecov.io/gh/LieberInstitute/spatialLIBD?branch=devel)\n[![R-CMD-check-bioc](https://github.com/LieberInstitute/spatialLIBD/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/LieberInstitute/spatialLIBD/actions/workflows/check-bioc.yml)\n[![GitHub issues](https://img.shields.io/github/issues/LieberInstitute/spatialLIBD)](https://github.com/LieberInstitute/spatialLIBD/issues)\n[![GitHub pulls](https://img.shields.io/github/issues-pr/LieberInstitute/spatialLIBD)](https://github.com/LieberInstitute/spatialLIBD/pulls)\n[![DOI](https://zenodo.org/badge/225913568.svg)](https://zenodo.org/badge/latestdoi/225913568)\n\n\n\u003c!-- badges: end --\u003e\n\nWelcome to the `spatialLIBD` project! It is composed of:\n\n* a [shiny](https://shiny.rstudio.com/) web application that we are hosting at [spatial.libd.org/spatialLIBD/](http://spatial.libd.org/spatialLIBD/) that can handle a [limited](https://github.com/LieberInstitute/spatialLIBD/issues/2) set of concurrent users,\n* a Bioconductor package at [bioconductor.org/packages/spatialLIBD](http://bioconductor.org/packages/spatialLIBD) (or from [here](http://research.libd.org/spatialLIBD/)) that lets you analyze the data and run a local version of our web application (with our data or yours),\n* and a [research article](https://doi.org/10.1038/s41593-020-00787-0) with the scientific knowledge we drew from this dataset. The analysis code for our project is available [here](https://github.com/LieberInstitute/HumanPilot/) and the high quality figures for the manuscript are available through [Figshare](https://doi.org/10.6084/m9.figshare.13623902.v1).\n\nThe web application allows you to browse the LIBD human dorsolateral pre-frontal cortex (DLPFC) spatial transcriptomics data generated with the 10x Genomics Visium platform. Through the [R/Bioconductor package](https://bioconductor.org/packages/spatialLIBD) you can also download the data as well as visualize your own datasets using this web application. Please check the [manuscript](https://doi.org/10.1038/s41593-020-00787-0) or [bioRxiv pre-print](https://www.biorxiv.org/content/10.1101/2020.02.28.969931v1) for more details about this project.\n\nIf you write about this website, the data or the R package please use\nthe \u003ccode\u003e\\#spatialLIBD\u003c/code\u003e hashtag. See previous tagged Bluesky posts \n\u003ca href=\"https://bsky.app/search?q=%23spatialLIBD\"\u003ehere\u003c/a\u003e.\nThank you!\n\n## Study design\n\nAs a quick overview, the data presented here is from portion of the DLPFC that spans six neuronal layers plus white matter (**A**) for a total of three subjects with two pairs of spatially adjacent replicates (**B**). Each dissection of DLPFC was designed to span all six layers plus white matter (**C**). Using this web application you can explore the expression of known genes such as _SNAP25_ (**D**, a neuronal gene), _MOBP_ (**E**, an oligodendrocyte gene), and known layer markers from mouse studies such as _PCP4_ (**F**, a known layer 5 marker gene).\n\n\u003cimg src=\"man/figures/paper_figure1.jpg\" align=\"center\" width=\"800px\" /\u003e\n\nThis web application was built such that we could annotate the spots to layers as you can see under the **spot-level data** tab. Once we annotated each spot to a layer, we compressed the information by a pseudo-bulking approach into **layer-level data**. We then analyzed the expression through a set of models whose results you can also explore through this web application. Finally, you can upload your own gene sets of interest as well as layer enrichment statistics and compare them with our LIBD Human DLPFC Visium dataset.\n\nIf you are interested in running this web application locally, you can do so thanks to the `spatialLIBD` R/Bioconductor package that powers this web application as shown below.\n\n```{r run_app, eval = FALSE}\n## Run this web application locally\nspatialLIBD::run_app()\n\n## You will have more control about the length of the\n## session and memory usage.\n\n## You could also use this function to visualize your\n## own data given some requirements described\n## in detail in the package vignette documentation\n## at http://research.libd.org/spatialLIBD/.\n```\n\n## Shiny website mirrors\n\n* [Main shiny application website](http://spatial.libd.org/spatialLIBD/) (note that the link must have a trailing slash `/` for it to work)\n* [Shinyapps](https://libd.shinyapps.io/spatialLIBD/) This version has less RAM memory but is typically deployed using the latest version of `spatialLIBD`.\n\n## Introductory material\n\nIf you prefer to watch a video overview of the `HumanPilot` project, check the following journal club presentation of the main results.\n\n\u003ciframe width=\"560\" height=\"315\" src=\"https://www.youtube.com/embed/qloLbG5-IPM?si=1gO1fujrgSXPfa6F\" title=\"YouTube video player\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen data-external=\"1\"\u003e\u003c/iframe\u003e\n\nYou might also be interested in the explainer video and [companion blog post](https://lcolladotor.github.io/2024/05/23/humanpilot-first-spatially-resolved-transcriptomics-study-using-visium/) as well as [the original Feb 29, 2020 blog post](https://lcolladotor.github.io/2020/02/29/diving-together-into-the-unknown-world-of-spatial-transcriptomics/) from when we first made this project public.\n\n\u003ciframe width=\"560\" height=\"315\" src=\"https://www.youtube.com/embed/HGioWKuI3ek?si=X-tqtZtcPSV-3uMt\" title=\"YouTube video player\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen data-external=\"1\"\u003e\u003c/iframe\u003e\n\n## R/Bioconductor package\n\nThe `spatialLIBD` package contains functions for:\n\n* Accessing the spatial transcriptomics data from the LIBD Human Pilot project ([code on GitHub](https://github.com/LieberInstitute/HumanPilot)) generated with the Visium platform from 10x Genomics. The data is retrieved from [Bioconductor](http://bioconductor.org/)'s `ExperimentHub`.\n* Visualizing the spot-level spatial gene expression data and clusters.\n* Inspecting the data interactively either on your computer or through [spatial.libd.org/spatialLIBD/](http://spatial.libd.org/spatialLIBD/).\n\nFor more details, please check the [documentation website](http://lieberinstitute.github.io/spatialLIBD) or the Bioconductor package landing page [here](https://bioconductor.org/packages/spatialLIBD).\n\n## Installation instructions\n\nGet the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `spatialLIBD` from [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(\"spatialLIBD\")\n```\n\nIf you want to use the development version of `spatialLIBD`, you will need to use the R version corresponding to the current Bioconductor-devel branch as described in more detail on the [Bioconductor website](http://bioconductor.org/developers/how-to/useDevel/). Then you can install `spatialLIBD` from GitHub using the following command.\n\n```{r \"install_devel\", eval = FALSE}\nBiocManager::install(\"LieberInstitute/spatialLIBD\")\n```\n\n\n\n## Access the data\n\nThrough the `spatialLIBD` package you can access the processed data in it's final R format. However, we also provide a table of links so you can download the raw data we received from 10x Genomics.\n\n### Processed data\n\nUsing `spatialLIBD` you can access the Human DLPFC spatial transcriptomics data from the 10x Genomics Visium platform. For example, this is the code you can use to access the layer-level data. For more details, check the help file for `fetch_data()`.\n\n```{r 'access_data', message=FALSE, fig.height = 8, fig.width = 9}\n## Load the package\nlibrary(\"spatialLIBD\")\n\n## Download the spot-level data\nspe \u003c- fetch_data(type = \"spe\")\n\n## This is a SpatialExperiment object\nspe\n\n## Note the memory size\nlobstr::obj_size(spe)\n\n## Remake the logo image with histology information\nvis_clus(\n    spe = spe,\n    clustervar = \"spatialLIBD\",\n    sampleid = \"151673\",\n    colors = libd_layer_colors,\n    ... = \" DLPFC Human Brain Layers\\nMade with research.libd.org/spatialLIBD/\"\n)\n```\n\n\n### Raw data\n\nYou can access all the raw data through [Globus](http://research.libd.org/globus/) (`jhpce#HumanPilot10x`). Furthermore, below you can find the links to the raw data we received from 10x Genomics.\n\n```{r 'AWS_links', eval = FALSE, echo = FALSE}\n## Read in the table of links from the HumanPilot repository\n## Since this depends on another repo, I set eval to FALSE.\naws_links \u003c-\n    read.table(\n        \"../HumanPilot/AWS_File_locations.tsv\",\n        header = TRUE,\n        stringsAsFactors = FALSE\n    )\n## Format into markdown links\nfor (i in seq_len(ncol(aws_links))[-1]) {\n    aws_links[[i]] \u003c- paste0(\"[AWS](\", aws_links[[i]], \")\")\n}\naws_links$`HTML_report` \u003c- paste0(\"[GitHub](https://github.com/LieberInstitute/HumanPilot/blob/master/10X/\", aws_links$SampleID, \"/\", aws_links$SampleID, \"_web_summary.html)\")\n\n## Print the table\nknitr::kable(aws_links, caption = \"Links to the Human DLPFC Visium raw data files\", format = \"markdown\")\n```\n\n| SampleID|h5_filtered                                                                                     |h5_raw                                                                                     |image_full                                                                           |image_hi                                                                                     |image_lo                                                                                      |loupe                                                                       |HTML_report                                                                                            |\n|--------:|:-----------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------------|:------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------|:------------------------------------------------------------------------------------------------------|\n|   151507|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151507_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151507_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_full_image.tif) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151507.cloupe) |[GitHub](https://github.com/LieberInstitute/HumanPilot/blob/master/10X/151507/151507_web_summary.html) |\n|   151508|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151508_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151508_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151508_full_image.tif) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151508_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151508_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151508.cloupe) |[GitHub](https://github.com/LieberInstitute/HumanPilot/blob/master/10X/151508/151508_web_summary.html) |\n|   151509|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151509_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151509_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151509_full_image.tif) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151509_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151509_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151509.cloupe) |[GitHub](https://github.com/LieberInstitute/HumanPilot/blob/master/10X/151509/151509_web_summary.html) |\n|   151510|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151510_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151510_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151510_full_image.tif) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151510_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151510_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151510.cloupe) |[GitHub](https://github.com/LieberInstitute/HumanPilot/blob/master/10X/151510/151510_web_summary.html) |\n|   151669|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151669_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151669_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151669_full_image.tif) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151669_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151669_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151669.cloupe) |[GitHub](https://github.com/LieberInstitute/HumanPilot/blob/master/10X/151669/151669_web_summary.html) |\n|   151670|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151670_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151670_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151670_full_image.tif) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151670_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151670_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151670.cloupe) |[GitHub](https://github.com/LieberInstitute/HumanPilot/blob/master/10X/151670/151670_web_summary.html) |\n|   151671|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151671_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151671_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151671_full_image.tif) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151671_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151671_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151671.cloupe) |[GitHub](https://github.com/LieberInstitute/HumanPilot/blob/master/10X/151671/151671_web_summary.html) |\n|   151672|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151672_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151672_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151672_full_image.tif) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151672_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151672_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151672.cloupe) |[GitHub](https://github.com/LieberInstitute/HumanPilot/blob/master/10X/151672/151672_web_summary.html) |\n|   151673|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151673_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151673_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151673_full_image.tif) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151673_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151673_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151673.cloupe) |[GitHub](https://github.com/LieberInstitute/HumanPilot/blob/master/10X/151673/151673_web_summary.html) |\n|   151674|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151674_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151674_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151674_full_image.tif) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151674_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151674_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151674.cloupe) |[GitHub](https://github.com/LieberInstitute/HumanPilot/blob/master/10X/151674/151674_web_summary.html) |\n|   151675|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151675_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151675_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151675_full_image.tif) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151675_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151675_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151675.cloupe) |[GitHub](https://github.com/LieberInstitute/HumanPilot/blob/master/10X/151675/151675_web_summary.html) |\n|   151676|[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151676_filtered_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/h5/151676_raw_feature_bc_matrix.h5) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151676_full_image.tif) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151676_tissue_hires_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151676_tissue_lowres_image.png) |[AWS](https://spatial-dlpfc.s3.us-east-2.amazonaws.com/loupe/151676.cloupe) |[GitHub](https://github.com/LieberInstitute/HumanPilot/blob/master/10X/151676/151676_web_summary.html) |\n\n## Citation\n\nBelow is the citation output from using `citation('spatialLIBD')` in R. Please \nrun this yourself to check for any updates on how to cite __spatialLIBD__.\n\n```{r 'citation', eval = requireNamespace('spatialLIBD')}\nprint(citation(\"spatialLIBD\"), bibtex = TRUE)\n```\n\nPlease note that the `spatialLIBD` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.\n\n## Code of Conduct\n  \nPlease note that the spatialLIBD 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## 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')`, `r BiocStyle::Githubpkg('r-hub/sysreqs')` 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/spatialLIBD) 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\n\n\u003ca href=\"https://www.libd.org/\"\u003e\u003cimg src=\"http://lcolladotor.github.io/img/LIBD_logo.jpg\" width=\"250px\"\u003e\u003c/a\u003e\n\n\u003ccenter\u003e\u003cscript type='text/javascript' id='clustrmaps' src='//cdn.clustrmaps.com/map_v2.js?cl=ffffff\u0026w=300\u0026t=n\u0026d=FRs8oQ9HVpMg6QLJJKAExpF8seGfPVlH-YOnwqUE8Hg'\u003e\u003c/script\u003e\u003c/center\u003e\n\n\u003c!-- Global site tag (gtag.js) - Google Analytics --\u003e\n\u003cscript async src=\"https://www.googletagmanager.com/gtag/js?id=G-QKT3SV9EFL\"\u003e\u003c/script\u003e\n\u003cscript\u003e\n  window.dataLayer = window.dataLayer || [];\n  function gtag(){dataLayer.push(arguments);}\n  gtag('js', new Date());\n\n  gtag('config', 'G-QKT3SV9EFL');\n\u003c/script\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flieberinstitute%2Fspatiallibd","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flieberinstitute%2Fspatiallibd","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flieberinstitute%2Fspatiallibd/lists"}