{"id":25138497,"url":"https://github.com/neurogenomics/mstexplorer","last_synced_at":"2025-04-24T03:08:22.223Z","repository":{"id":46023646,"uuid":"413778458","full_name":"neurogenomics/MSTExplorer","owner":"neurogenomics","description":"Multi-Scale Target Explorer systematically identifies, prioritises, and visualises cell-type-specific gene therapy targets across the phenome.","archived":false,"fork":false,"pushed_at":"2025-03-11T13:29:50.000Z","size":9503,"stargazers_count":2,"open_issues_count":3,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-04-24T03:08:16.518Z","etag":null,"topics":["biomedicine","cell-types","enrichment-analysis","genetics","human-phenotype-ontology","parallel-computing","r-package","rare-disease"],"latest_commit_sha":null,"homepage":"https://neurogenomics.github.io/MSTExplorer/","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":"NEWS.md","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":"2021-10-05T10:54:39.000Z","updated_at":"2025-03-09T05:45:38.000Z","dependencies_parsed_at":"2022-08-19T08:40:43.301Z","dependency_job_id":"a1ab0406-90ee-47ef-8e43-03d6d133009f","html_url":"https://github.com/neurogenomics/MSTExplorer","commit_stats":null,"previous_names":["neurogenomics/mstexplorer"],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurogenomics%2FMSTExplorer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurogenomics%2FMSTExplorer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurogenomics%2FMSTExplorer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/neurogenomics%2FMSTExplorer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/neurogenomics","download_url":"https://codeload.github.com/neurogenomics/MSTExplorer/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250552074,"owners_count":21449164,"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":["biomedicine","cell-types","enrichment-analysis","genetics","human-phenotype-ontology","parallel-computing","r-package","rare-disease"],"created_at":"2025-02-08T17:16:49.760Z","updated_at":"2025-04-24T03:08:22.215Z","avatar_url":"https://github.com/neurogenomics.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\ntitle: \"`r read.dcf('DESCRIPTION', fields = 'Package')[1]`\"  \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\u003c!-- To modify Package/Title/Description/Authors fields, edit the DESCRIPTION file --\u003e\n\n```{r, echo=FALSE, include=FALSE}\npkg \u003c- read.dcf(\"DESCRIPTION\", fields = \"Package\")[1]\ntitle \u003c- read.dcf(\"DESCRIPTION\", fields = \"Title\")[1]\ndescription \u003c- gsub(\"\\n\",\" \",read.dcf(\"DESCRIPTION\", fields = \"Description\")[1])\nURL \u003c- read.dcf('DESCRIPTION', fields = 'URL')[1]\nowner \u003c- strsplit(URL,\"/\")[[1]][4]\nrepo \u003c-strsplit(URL,\"/\")[[1]][5]\n```\n \n## Introduction\n\nMany genes have been associated with diseases \nMulti-Scale Target Explorer (`MSTExplorer`) systematically identifies, prioritises, and visualises cell-type-specific gene therapy targets across the phenome. \n\nCore functionalities include:  \n\n**1. Conducting phenotype x cell type genetic association tests at scale**\n  \n  - The [Human Phenotype Ontology](https://hpo.jax.org/) (integrated with gene annotations from [OMIM](https://omim.org/) / [DECIPHER](https://www.deciphergenomics.org/) / [ORPHANET](https://www.orpha.net/)) is used as the source of phenotype gene signatures. Each gene-phenotype associated is given a continuous score that approximates the current strength of evidence for the association (using data derived from [GenCC](https://thegencc.org/)).  \n    \n  - Whole-body scRNA-seq atlases from humans (across multiple developmental stages) are used as a data-driven source of cell type-specific gene markers.  \n  - The underlying association tests are designed for both speed and accuracy using memory-efficient data structures, and a highly parallelisable implementation of Generalised Linear Regression (GLM). For example, associations for all pairwise combinations of \u003e11k phenotypes x \u003e200 cell types (\u003e2,200,000 associations) can be in \u003c30 minutes on a Macbook laptop with 10 CPU cores).\n\n**2. Inferring multi-scale causal graphs of disease**\n\n`MSTExplorer` allows users to easily infer and construct multi-scale causal graphs of Diseases (blue nodes) -\u003e Phenotypes (purple nodes) -\u003e Cell types (orange nodes) -\u003e Genes (yellow nodes).  \n\n![*Example multi-scale network focused on lethal skeletal dysplasia, a phenotype of multiple diseases*](https://github.com/neurogenomics/rare_disease_celltyping/blob/299abe0ccd00644bc2f05a1389704fe196a3e868/manuscript/_manuscript/img/fig-therapy-examples-supp/lethal_skeletal_dysplasia.png?raw=true){height=400px}\n\n[See here for more example networks.](https://github.com/neurogenomics/rare_disease_celltyping/tree/299abe0ccd00644bc2f05a1389704fe196a3e868/manuscript/_manuscript/img/fig-therapy-examples-supp).\n\n**3. Prioritising cell-type-specific gene therapy targets**\n\n`MSTExplorer` also provides a comprehensive and customisable pipeline that can be run via a single function (`prioritise_targets()`) to produce the most promising cell-type-specific gene therapy targets across the phenome.\n\n## Installation \n\nWithin R: \n\n```R\nif(!require(\"BiocManager\")) install.packages(\"BiocManager\")\n\nBiocManager::install(\"`r paste(owner,repo,sep='/')`\")\nlibrary(`r pkg`)\n```\n\n## Documentation \n\n#### [Website](https://`r owner`.github.io/`r pkg`) \n#### [Get started](https://`r owner`.github.io/`r pkg`/articles/`r pkg`)\n#### [Docker/Singularity Container](https://`r owner`.github.io/`r pkg`/articles/docker.html)\n\n## Citation\n\nIf you use ``r pkg``, please cite: \n\n\u003c!-- Modify this by editing the file: inst/CITATION  --\u003e\n\u003e `r utils::citation(pkg)$textVersion`\n\n## Contact\n\n### [Neurogenomics Lab](https://www.neurogenomics.co.uk)   \nUK Dementia Research Institute  \nDepartment of Brain Sciences  \nFaculty of Medicine  \nImperial College London  \n[GitHub](https://github.com/neurogenomics)\n\n## Session Info \n\n\u003cdetails\u003e \n\n```{r Session Info}\nutils::sessionInfo()\n```\n\n\u003c/details\u003e  \n\u003chr\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneurogenomics%2Fmstexplorer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fneurogenomics%2Fmstexplorer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneurogenomics%2Fmstexplorer/lists"}