{"id":22632093,"url":"https://github.com/alleninstitute/l5_ven","last_synced_at":"2025-04-11T20:11:50.715Z","repository":{"id":145221285,"uuid":"174621868","full_name":"AllenInstitute/L5_VEN","owner":"AllenInstitute","description":"This repository contains code for reproducing the analysis of snRNA-seq data from human fronto-insula","archived":false,"fork":false,"pushed_at":"2022-07-27T17:25:59.000Z","size":14697,"stargazers_count":6,"open_issues_count":0,"forks_count":3,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-11T20:11:46.466Z","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":"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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-03-08T22:54:18.000Z","updated_at":"2024-11-14T05:12:08.000Z","dependencies_parsed_at":null,"dependency_job_id":"d88292c9-273f-4a78-a6c6-925558d44c86","html_url":"https://github.com/AllenInstitute/L5_VEN","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2FL5_VEN","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2FL5_VEN/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2FL5_VEN/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AllenInstitute%2FL5_VEN/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AllenInstitute","download_url":"https://codeload.github.com/AllenInstitute/L5_VEN/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248473129,"owners_count":21109628,"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":"2024-12-09T02:15:56.841Z","updated_at":"2025-04-11T20:11:50.707Z","avatar_url":"https://github.com/AllenInstitute.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# VENcelltypes\nThis repository contains code for reproducing the analysis of snRNA-seq data from human fronto-insula described in [Hodge, Miller, et al 2020](https://www.nature.com/articles/s41467-020-14952-3).\n\nWhile this is set up as an R library for convenience, it is really just a wrapper for the analysis functions and does not follow all of the conventions of R libraries (function annotation, unit testing, etc.).  Please be sure to cite the appropriate other R libraries if replicating the code.  \n\nInstall using:\n```\ndevtools::install_github(\"AllenInstitute/VENcelltypes\")\n```\n\nThere are several dependencies listed in the code books below, but one notable one is that [version **3.0** of Seurat](https://satijalab.org/seurat/pancreas_integration_label_transfer.html) needs to be installed.\n```\ndevtools::install_github(repo = \"satijalab/seurat\", ref = \"release/3.0\")\n```\n\n## Code book\n\nTo replicate the figures in the paper, please use the code below:\n\n1. **Code 1. Download and prepare the data** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/VENcelltypes/blob/master/vignettes/Code1_prepareComparisonDataSets.nb.html)  This script reads converts data downloaded from the [Allen Institute Cell Types Database](http://celltypes.brain-map.org/rnaseq) into a format compatible for use as comparison data to human fronto-insula.  \n2. **Code 2. Rename clusters and build tree** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/VENcelltypes/blob/master/vignettes/Code2_clusterNames_buildTree_Fig1.nb.html)  This script reads in the data and assigned clusters, organizes the clusters into a dendrogram, renames the clusters to include class information and informative genes, and then plots some summary plots.  \n3. **Code 3. Quality control assessment** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/VENcelltypes/blob/master/vignettes/Code3_QC_assessment_FigS1.nb.html)  This script reads in the data output to the feather files and uses it to calculate and plot some QC information for Supplementary figure 1.  \n4. **Code 4. Cross-species analysis** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/VENcelltypes/blob/master/vignettes/Code4_crossSpeciesComparisons.nb.html)  This script performs alignment of deep excitatory neurons in human fronto-insula, human middle temporal gyrus, mouse primary visual cortex, and mouse anterior lateral motor cortex.  It also identifies genes with common and distinct patterning across these data sets.  \n5. **Code 5. Human FI vs. Human MTG comparison** [(LINK TO SCRIPT)](http://htmlpreview.github.io/?https://github.com/AllenInstitute/VENcelltypes/blob/master/vignettes/Code5_humanMTGvsFI.nb.html)  This script identifies common and distinct CF-associated genes in human middle temporal gyrus as compared with human fronto-insula, and compares the proportions of cells across clusters for each brain region.  \n\nAll code was tested in both a UNIX and Windows environment and show to produce the same result, with the exception of the UMAP visualization noted in Code 4.\n\nPlease e-mail jeremym@alleninstitute.org with any issues.\n\n## License\n\nThe license for this package is available on Github at: https://github.com/AllenInstitute/VENcelltypes/blob/master/LICENSE\n\n## Level of Support\n\nThis code will be updated only if figures change during review.\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/VENcelltypes/blob/master/CONTRIBUTION\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falleninstitute%2Fl5_ven","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falleninstitute%2Fl5_ven","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falleninstitute%2Fl5_ven/lists"}