{"id":22631913,"url":"https://github.com/alleninstitute/scrattch.mapping","last_synced_at":"2025-09-14T04:33:13.868Z","repository":{"id":216009848,"uuid":"572210148","full_name":"AllenInstitute/scrattch.mapping","owner":"AllenInstitute","description":"Genearlized mapping scripts for RNA-seq and Patch-seq data","archived":false,"fork":false,"pushed_at":"2025-05-14T22:49:40.000Z","size":4320,"stargazers_count":15,"open_issues_count":9,"forks_count":3,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-09-09T04:22:26.608Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/AllenInstitute.png","metadata":{"files":{"readme":"README.md","changelog":null,"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":"2022-11-29T19:33:57.000Z","updated_at":"2025-06-30T06:36:23.000Z","dependencies_parsed_at":"2024-01-09T02:57:58.533Z","dependency_job_id":"f045fc3d-25ee-478f-a669-73300bb1918d","html_url":"https://github.com/AllenInstitute/scrattch.mapping","commit_stats":null,"previous_names":["alleninstitute/scrattch.mapping"],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/AllenInstitute/scrattch.mapping","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fscrattch.mapping","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fscrattch.mapping/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fscrattch.mapping/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fscrattch.mapping/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AllenInstitute","download_url":"https://codeload.github.com/AllenInstitute/scrattch.mapping/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fscrattch.mapping/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":275062953,"owners_count":25398886,"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":"2025-09-14T02:00:10.474Z","response_time":75,"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":[],"created_at":"2024-12-09T02:14:11.118Z","updated_at":"2025-09-14T04:33:13.826Z","avatar_url":"https://github.com/AllenInstitute.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# scrattch.mapping\n\nGeneralized mapping scripts for RNA-seq, Patch-seq or any gene expression data. Assumes that you have built an Allen Institute Taxonomy (AIT) object with [scrattch.taxonomy](https://github.com/AllenInstitute/scrattch.taxonomy).\n\n## Documentation\n\nYou can find a detail description of all scrattch.mapping functions here: ![Documentation](https://github.com/AllenInstitute/scrattch-mapping/blob/main/scrattch.mapping_0.1.pdf)\n\nUpdate notes are here: ![Versions](https://github.com/AllenInstitute/scrattch-mapping/blob/dev_njj/VERSIONS.md)\n\n## Installation\n\n### Using docker (recommended)\nWe have setup a docker environment for scrattch.taxonomy, scrattch.mapping, and scrattch.patchseq that contains all the required dependencies and the current version of all scrattch packages. **See [the readme](https://github.com/AllenInstitute/scrattch/blob/master/README.md#using-docker) for [the parent scrattch package](https://github.com/AllenInstitute/scrattch) for the most up-to-date docker information.**\n\n### Directly from GitHub (strongly discouraged)\n\nWhile we advise using the provided docker, you can also install scrattch.mapping directly from GitHub as follows:\n\n```\ndevtools::install_github(\"AllenInstitute/scrattch.mapping\")\n```\n\nThis strategy **might not work** due to complicated dependencies. Also note that `doMC` may need to be installed manually from [HERE](https://r-forge.r-project.org/R/?group_id=947) if you use Windows. Vignettes are provided below.\n\n## Usage examples\n\n1. [**Run Flat, Tree, and Seurat taxonomy mapping**](https://github.com/AllenInstitute/scrattch-mapping/blob/main/examples/mapping.md) This examples shows how to use scrattch.mapping for standard taxonomy mapping.\n2. [**Mapping to HMBA Basal Ganglia AIT**](https://github.com/AllenInstitute/scrattch-mapping/blob/main/examples/mapping_BasalGanglia.md) This tutorial shows how to map against the HMBA Human and Macaque Basal Ganglia consensus taxonomies.\n\n## Reporting issues\n\nIf you run into any issues, please let Nelson and Jeremy know or [**create a new issue in the 'Issues' tab above**](https://github.com/AllenInstitute/scrattch-mapping/issues).\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falleninstitute%2Fscrattch.mapping","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falleninstitute%2Fscrattch.mapping","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falleninstitute%2Fscrattch.mapping/lists"}