{"id":25138521,"url":"https://github.com/neurogenomics/magma_celltyping","last_synced_at":"2025-10-16T23:19:28.852Z","repository":{"id":44742628,"uuid":"132120322","full_name":"neurogenomics/MAGMA_Celltyping","owner":"neurogenomics","description":"Find causal cell-types underlying complex trait genetics","archived":false,"fork":false,"pushed_at":"2025-02-25T16:21:20.000Z","size":259909,"stargazers_count":82,"open_issues_count":11,"forks_count":32,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-03-30T19:05:06.346Z","etag":null,"topics":["genomics","gwas","magma","single-cell","single-cell-omics","snps","statistical-genetics"],"latest_commit_sha":null,"homepage":"https://neurogenomics.github.io/MAGMA_Celltyping","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/neurogenomics.png","metadata":{"files":{"readme":"README.Rmd","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}},"created_at":"2018-05-04T09:38:10.000Z","updated_at":"2025-03-19T21:20:29.000Z","dependencies_parsed_at":"2023-10-20T23:15:23.261Z","dependency_job_id":null,"html_url":"https://github.com/neurogenomics/MAGMA_Celltyping","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/neurogenomics%2FMAGMA_Celltyping","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurogenomics%2FMAGMA_Celltyping/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurogenomics%2FMAGMA_Celltyping/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurogenomics%2FMAGMA_Celltyping/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/neurogenomics","download_url":"https://codeload.github.com/neurogenomics/MAGMA_Celltyping/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247543589,"owners_count":20955865,"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":["genomics","gwas","magma","single-cell","single-cell-omics","snps","statistical-genetics"],"created_at":"2025-02-08T17:16:53.688Z","updated_at":"2025-10-16T23:19:23.815Z","avatar_url":"https://github.com/neurogenomics.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\ntitle: \"\"  \nauthor: \"`r rworkflows::use_badges()`\"\ndate: \"\u003ch4\u003eREADME updated: \u003ci\u003e`r format( Sys.Date(), '%b-%d-%Y')`\u003c/i\u003e\u003c/h4\u003e\"\noutput:\n  github_document\n---\n\n```{r, echo=FALSE, include=FALSE}\npkg \u003c- read.dcf(\"DESCRIPTION\", fields = \"Package\")[1]\nrepo \u003c- gsub(\"https://github.com/\",\"\",\n            read.dcf('DESCRIPTION', fields = 'URL')) \ndescription \u003c- read.dcf(\"DESCRIPTION\", fields = \"Description\")[1]\n```\n\n## Introduction\n\nThis R package contains code used for testing which cell types can explain the heritability signal from GWAS summary statistics. The method was described in our [2018 Nature Genetics paper](https://www.nature.com/articles/s41588-018-0129-5). \n\nThis package takes GWAS summary statistics + single-cell transcriptome specificity data (in [EWCE](https://github.com/NathanSkene/EWCE)'s CellTypeData format) as input. It then calculates and returns the enrichment between the GWAS trait and the cell-types. \n\n## Installation\n\n### R\n\nInstall `MAGMA.Celltyping` as follows:\n\n```R\nif(!require(\"remotes\")) install.packages(\"remotes\")\n\nremotes::install_github(\"`r repo`\")\nlibrary(`r pkg`)\n```\n\n### MAGMA \n\n`MAGMA.Celltyping` now installs the command line software MAGMA automatically\nwhen you first use a function that relies on [MAGMA](https://ctg.cncr.nl/software/magma) (e.g. `celltype_associations_pipeline`). \nIf you prefer, you can later install other versions of MAGMA with:\n\n```R\nMAGMA.Celltyping::install_magma(desired_version=\"\u003cversion\u003e\",\n                                update = TRUE)\n```  \n\n## Documentation \n\n### [Website](https://neurogenomics.github.io/MAGMA_Celltyping/)\n\n### [Getting started](https://neurogenomics.github.io/MAGMA_Celltyping/articles/MAGMA.Celltyping.html)\n\n### [Docker/Singularity](https://neurogenomics.github.io/MAGMA_Celltyping/articles/docker)\n\n\n## Using older versions\n\nWith the release of `MAGMA_Celltyping` 2.0 in January 2022, there have been a number of [major updates and bug fixes](https://github.com/neurogenomics/MAGMA_Celltyping/pull/93). \n\n- Only R\u003e4.0.0 is supported. To use this package with older versions of R, install with:`remotes::install_github(\"neurogenomics/MAGMA_Celltyping@01a9e53\")` \n\n## Bugs/fixes\n\nHaving trouble? Search the [Issues](https://github.com/neurogenomics/MAGMA_Celltyping/issues) \nor submit a new one.\n\nWant to contribute new features/fixes? [Pull Requests](https://github.com/neurogenomics/MAGMA_Celltyping/pulls) are welcomed!\n\nBoth are most welcome, we want the package to be easy to use for everyone!\n\n## Citations\n\nIf you use the software then please cite:  \n\n\u003e [Skene, et al. Genetic identification of brain cell types underlying schizophrenia. Nature Genetics, 2018.](https://www.nature.com/articles/s41588-018-0129-5)\n\nThe package utilises the [MAGMA](https://ctg.cncr.nl/software/magma) software developed in the Complex Trait Genetics Lab at VU university (not us!) so please also cite:  \n\n\u003e [de Leeuw, et al. MAGMA: Generalized gene-set analysis of GWAS data. PLoS Comput Biol, 2015.](https://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1004219)\n\nIf you use the EWCE package as well then please cite:  \n\n\u003e [Skene, et al. Identification of Vulnerable Cell Types in Major Brain Disorders Using Single Cell Transcriptomes and Expression Weighted Cell Type Enrichment. Front. Neurosci, 2016.](https://www.frontiersin.org/articles/10.3389/fnins.2016.00016/full)\n\nIf you use `MungeSumstats` to format your summary statistics then please cite:\n\n\u003e [Murphy, Schilder, \u0026 Skene, MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics, Bioinformatics, Volume 37, Issue 23, 1 December 2021, Pages 4593–4596, https://doi.org/10.1093/bioinformatics/btab665](https://doi.org/10.1093/bioinformatics/btab665)  \n\nIf you use the cortex/hippocampus single cell data associated with this package then please cite the following papers:\n\n\u003e [Zeisel, et al. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science, 2015.](https://doi.org/10.1126/science.aaa1934)\n\nIf you use the midbrain and hypothalamus single cell datasets associated with the 2018 paper then please cite the following papers:\n\n\u003e [La Manno, et al. Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells. Cell, 2016.](https://doi.org/10.1016/j.cell.2016.09.027)\n\n\u003e [Romanov, et al. Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes. Nature Neuroscience, 2016.](https://doi.org/10.1038/nn.4462)\n\n\u003chr\u003e\n\n## Contact\n \n### [Neurogenomics Lab](https://www.neurogenomics.co.uk/)\n\nUK Dementia Research Institute  \nDepartment of Brain Sciences  \nFaculty of Medicine  \nImperial College London   \n[GitHub](https://github.com/neurogenomics)  \n[DockerHub](https://hub.docker.com/orgs/neurogenomicslab)  \n\n\u003cbr\u003e\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneurogenomics%2Fmagma_celltyping","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fneurogenomics%2Fmagma_celltyping","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneurogenomics%2Fmagma_celltyping/lists"}