{"id":17686953,"url":"https://github.com/benfulcher/mousegradients","last_synced_at":"2025-05-13T00:41:09.732Z","repository":{"id":70978685,"uuid":"169654485","full_name":"benfulcher/mouseGradients","owner":"benfulcher","description":"Code to reproduce analyses of mouse cortical gradients","archived":false,"fork":false,"pushed_at":"2019-02-27T06:38:32.000Z","size":2464,"stargazers_count":9,"open_issues_count":0,"forks_count":5,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-01T05:11:29.996Z","etag":null,"topics":["geneexpression","mouse","neuroscience"],"latest_commit_sha":null,"homepage":null,"language":"MATLAB","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/benfulcher.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}},"created_at":"2019-02-07T22:43:06.000Z","updated_at":"2023-12-12T01:28:51.000Z","dependencies_parsed_at":null,"dependency_job_id":"646bc08c-28b2-46b4-8424-2d73e086e7fa","html_url":"https://github.com/benfulcher/mouseGradients","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benfulcher%2FmouseGradients","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benfulcher%2FmouseGradients/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benfulcher%2FmouseGradients/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/benfulcher%2FmouseGradients/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/benfulcher","download_url":"https://codeload.github.com/benfulcher/mouseGradients/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253850841,"owners_count":21973667,"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":["geneexpression","mouse","neuroscience"],"created_at":"2024-10-24T10:46:30.820Z","updated_at":"2025-05-13T00:41:09.720Z","avatar_url":"https://github.com/benfulcher.png","language":"MATLAB","funding_links":[],"categories":[],"sub_categories":[],"readme":"# mouseGradients\n\nThis repository contains code to reproduce all figures from our paper:\n\nFulcher, B. D., Murray, J. D., Zerbi, V., \u0026 Wang, X.-J. (2019).\n[Multimodal gradients across mouse cortex](http://doi.org/10.1073/pnas.1814144116).\nPNAS, 201814144.\n\n## Downloading processed data\nYou will need to fill the `Data` directory with some processed data that you can download from [this figshare repository](https://figshare.com/articles/Mouse_cortical_gradients/7775684).\n\nThis paper would not have been possible without the generous sharing of open data (thank you!).\nPlease consult each original data source for detailed licensing information for each dataset.\n\nAllen Institute gene-expression data was retrieved using [custom code](https://github.com/benfulcher/AllenSDK) that queries the [Allen SDK](https://github.com/AllenInstitute/AllenSDK).\n\n## Figures\n\nFigure 1A generated manually mouse-brain imaging software (by Valerio Zerbi).\n\n### Figure 1B: T1w:T2w across all brain areas\n\n```matlab\nFunctionalClasses()\n```\n![Results](FigureOutputs/FunctionalClasses.png)\n\n### Figure 1C-F: Scatter plots versus T1w:T2w\n\n```matlab\nT1T2Corrs()\n```\n![Results](FigureOutputs/T1T2_Correlations.png)\n\n### Figure 2A,B: Zooming in on some manually-selected genes\n\n```matlab\nSpecificGeneFigure()\n```\n\nNote that B was removed from the final paper; which only plots the _Grin3a_ scatter\n![Results](FigureOutputs/SpecificGenes.png)\n\n### Figure 2C: Low-dimensional projection\n\n```matlab\nMassAction('brainExpressed','scaledSigmoid','benCombo','bayesian')\n```\n\nNote that additional outputs are also produced, visualizing analytics about the principal components, including Fig.S4.\n![Results](FigureOutputs/LowDimProjection.png)\n\n\n### Figure 3: Correlations across individual cortical layers\n\n```matlab\nLaminarPlot()\n```\n\n![Results](FigureOutputs/LaminarPlot.png)\n\n### Figure 4: Combination of diverse measurements\n\n```matlab\nDiverseMatrixT1T2()\nPlotBigDamnMatrix()\n```\n\n![Results](FigureOutputs/AllTogetherNow.png)\n\n\n### Figure 5: Interspecies comparison\n\n```matlab\nG = LoadMeG('cortexAll');\nHumanMouseComparisonAnal(G,'brainRelated','benCombo',true)\n```\n\n![Results](FigureOutputs/InterSpeciesPlot.png)\n\n## Supplementary Figures\n\nFigs S1, S2, S3 generated manually using mouse-brain imaging software (by Valerio Zerbi).\n\n### Figure S4: Correlations of T1w:T2w with Principal Component projections of brain-expressed genes\n```matlab\nMassAction('brainExpressed','scaledSigmoid','benCombo','bayesian')\n```\n![Results](FigureOutputs/T1T2_PC_correlations.png)\n\n\n### Figure S5: Correlations between T1w:T2w values measured in individual cortical layers\n```matlab\nT1T2ByLayer\n```\n![Results](FigureOutputs/T1T2ByLayer.png)\n\n### Figure S6: Correlations to Ero et al. (2019) cell-density estimates\n```matlab\nMyelinCorrs('CellAtlas')\n```\n![Results](FigureOutputs/CellAtlasCorrelations.png)\n\n### Figure S7: Layer-specific gene-expression gradients\n\n```matlab\nTheBestLayers('genes',true,[]);\n```\n\n![Results](FigureOutputs/T1T2_geneAllLayers.png)\n\n### Figure S8: Comparison of Harris hierarchy and T1w:T2w\n\n```matlab\nT1T2_or_hierarchy\n```\n\n![Results](FigureOutputs/T1wT2w_hierarchy.png)\n\n### Figure S9: Comparison of mouse-human correspondence as a function of expression processing and gene-set filtering\n\n```matlab\nwhatGeneSets = {'all','brainExpressed','brainRelated','CahoyNeuron','CahoyOgligodendrocyte','CahoyAstrocyte','myelinSetOf999'};\nwhatSectionFilters = {'sagittal','coronal','combZ','benCombo','replicated'};\nHumanMouseSectionCompare(whatGeneSets,whatSectionFilters);\n```\n\n![Results](FigureOutputs/mouseHumanCorrCompare.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbenfulcher%2Fmousegradients","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbenfulcher%2Fmousegradients","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbenfulcher%2Fmousegradients/lists"}