{"id":22632090,"url":"https://github.com/alleninstitute/mfishtools","last_synced_at":"2026-01-07T21:33:02.217Z","repository":{"id":42124065,"uuid":"136991200","full_name":"AllenInstitute/mfishtools","owner":"AllenInstitute","description":"Building Gene Sets and Mapping mFISH Data","archived":false,"fork":false,"pushed_at":"2023-06-08T19:03:58.000Z","size":2174,"stargazers_count":16,"open_issues_count":1,"forks_count":6,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-02-03T14:14:42.495Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"HTML","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/AllenInstitute.png","metadata":{"files":{"readme":"README.md","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}},"created_at":"2018-06-11T23:19:09.000Z","updated_at":"2024-04-26T10:52:19.000Z","dependencies_parsed_at":"2023-10-20T16:43:28.473Z","dependency_job_id":null,"html_url":"https://github.com/AllenInstitute/mfishtools","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fmfishtools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fmfishtools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fmfishtools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2Fmfishtools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AllenInstitute","download_url":"https://codeload.github.com/AllenInstitute/mfishtools/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246137215,"owners_count":20729324,"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":[],"created_at":"2024-12-09T02:15:54.499Z","updated_at":"2026-01-07T21:33:02.212Z","avatar_url":"https://github.com/AllenInstitute.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"*(See a better-formatted version of this page at https://alleninstitute.github.io/mfishtools/)*\n\n# mfishtools\n\nR functions for gene selection and analysis of mFISH data\n\nmfishtools includes many functions that are used for analysis of data for the CZI SpaceTx project, and mostly relies on correlation-based analysis with filtering.  *This library is still in beta testing and may be buggy.  Community involvement is encouraged through both issues and pull requests.*  \n\n## Installation\n\nInstall prerequisites:\n```\ninstall.packages(\"devtools\")\ndevtools::install_github(\"AllenInstitute/scrattch.vis\")\ndevtools::install_github(\"AllenInstitute/tasic2016data\")\n```\n\nNote that some people may need to manually install the `GO.db` and `WGCNA` libraries as well:\n```\ninstall.packages(\"BiocManager\")\nBiocManager::install(\"GO.db\")\nBiocManager::install(\"WGCNA\")\n```\n\nInstall `mfishtools` using:\n```\n# Quickly, but without the vignettes:\ndevtools::install_github(\"AllenInstitute/mfishtools\")\n\n# More slowly, but with the vignettes:\ninstall.packages(\"remotes\", repos='http://cran.us.r-project.org')\nremotes::install_github(\"AllenInstitute/mfishtools\", build_vignettes = TRUE)\n```\n\n\n## Library use cases\n\nThere are two primary use cases for this libary:\n\n1. **Building a combinatorial marker gene panel for spatial transcriptomics.** [LINK TO VIGNETTE](http://htmlpreview.github.io/?https://github.com/AllenInstitute/mfishtools/blob/master/vignettes/inhibitory_marker_selection.html)  This allows the generation of computationally \"optimal\" marker gene panels based on single cell/nucleus RNA-Seq reference data.  A starting set of manually-selected marker genes is first selected, and then the remaining genes are chosen using a greedy algorithm.  Relevant statistics and plots are generated that show the predicted success for the panel.  \n2. **Mapping cells from spatial transcriptomics data sets to reference cell types.** [LINK TO VIGNETTE](http://htmlpreview.github.io/?https://github.com/AllenInstitute/mfishtools/blob/master/vignettes/inhibitory_marker_mapping.html)  This allows for cell type calling of cells in a spatial transcriptomics study, and also predicts the accuracy of the calls based on reference data.  *Note: it is currently unclear how reliable this method is at correctly predicting cell type calls.  Please review results carefully!*  Plots can also be generated to show the results.  \n\nMany functions are currently not included in these vignettes; please use the R help (\"?\") if additional information is needed, or e-mail me at jeremym@alleninstitute.org.\n\n## License\n\nThe license for this package is available on Github at: https://github.com/AllenInstitute/mfishtools/blob/master/LICENSE\n\n## Level of Support\n\nWe are planning on occasional updating this tool with no fixed schedule. Community involvement is encouraged through both issues and pull requests.\n\n## Contribution Agreement\n\nIf you contribute code to this repository through pull requests or other mechanisms, you are subject to the Allen Institute Contribution Agreement, which is available in full at: https://github.com/AllenInstitute/mfishtools/blob/master/CONTRIBUTION\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falleninstitute%2Fmfishtools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falleninstitute%2Fmfishtools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falleninstitute%2Fmfishtools/lists"}