{"id":24528924,"url":"https://github.com/saezlab/visiumms","last_synced_at":"2025-04-14T17:10:46.276Z","repository":{"id":77872981,"uuid":"404092512","full_name":"saezlab/VisiumMS","owner":"saezlab","description":"Study of Multiple Sclerosis(MS) using paried snRNA-seq and Visium transcriptmics datasets.","archived":false,"fork":false,"pushed_at":"2024-12-11T21:18:59.000Z","size":44607,"stargazers_count":7,"open_issues_count":1,"forks_count":5,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-28T05:51:06.321Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/saezlab.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":"2021-09-07T19:02:54.000Z","updated_at":"2025-03-13T16:56:15.000Z","dependencies_parsed_at":"2024-06-13T12:15:56.612Z","dependency_job_id":"ebc68ed4-58c0-40f6-89ac-e2959b557db0","html_url":"https://github.com/saezlab/VisiumMS","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/saezlab%2FVisiumMS","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FVisiumMS/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FVisiumMS/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FVisiumMS/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/VisiumMS/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248923764,"owners_count":21183954,"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":"2025-01-22T07:34:00.114Z","updated_at":"2025-04-14T17:10:46.246Z","avatar_url":"https://github.com/saezlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# VisiumMS\nScripts to reproduce results from \"Spatial cell type mapping of multiple sclerosis lesions\".\n\nThis pipeline uses `Snakemake` to ensure reproducibility\n\n## Data\nProcessed data in `h5ad` format can be downloaded from the Human Cell Atlas [portal](https://explore.data.humancellatlas.org/projects/4c8e9d75-d85a-47de-9598-06549cf44b91), while raw data is available on [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE279183).\n\n## Installation\n\nClone repo:\n```\ngit clone git@github.com:saezlab/VisiumMS.git\ncd VisiumMS\n```\n\nInstall `mamba` (this might take a while) to install packages faster:\n```\nconda install -n base -c conda-forge mamba\n```\n\nThen create a new enviroment specific for `Snakemake`:\n```\nmamba create -c conda-forge -c bioconda -n snakemake snakemake\nconda activate snakemake\n```\n\nTo run specific outputs you can run:\n```\nsnakemake --profile config/slurm/  path/to/output/file \n```\n\nTo run the complete processing of the data (this can take a while), run:\n```\nsnakemake --profile config/slurm/\n```\n\n## Reference\nLerma-Martin, C., Badia-i-Mompel, P., Ramirez Flores, R.O. et al. Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions. Nat Neurosci 27, 2354–2365 (2024). https://doi.org/10.1038/s41593-024-01796-z\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fvisiumms","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fvisiumms","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fvisiumms/lists"}