https://github.com/neurogenomics/mstexplorer
Multi-Scale Target Explorer systematically identifies, prioritises, and visualises cell-type-specific gene therapy targets across the phenome.
https://github.com/neurogenomics/mstexplorer
biomedicine cell-types enrichment-analysis genetics human-phenotype-ontology parallel-computing r-package rare-disease
Last synced: about 2 months ago
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Multi-Scale Target Explorer systematically identifies, prioritises, and visualises cell-type-specific gene therapy targets across the phenome.
- Host: GitHub
- URL: https://github.com/neurogenomics/mstexplorer
- Owner: neurogenomics
- Created: 2021-10-05T10:54:39.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2025-03-11T13:29:50.000Z (3 months ago)
- Last Synced: 2025-04-24T03:08:16.518Z (about 2 months ago)
- Topics: biomedicine, cell-types, enrichment-analysis, genetics, human-phenotype-ontology, parallel-computing, r-package, rare-disease
- Language: R
- Homepage: https://neurogenomics.github.io/MSTExplorer/
- Size: 9.06 MB
- Stars: 2
- Watchers: 2
- Forks: 2
- Open Issues: 3
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
Awesome Lists containing this project
README
---
title: "`r read.dcf('DESCRIPTION', fields = 'Package')[1]`"
author: "`r rworkflows::use_badges()`"
date: "
README updated: `r format( Sys.Date(), '%b-%d-%Y')`
"
output:
github_document
---
```{r, echo=FALSE, include=FALSE}
pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
title <- read.dcf("DESCRIPTION", fields = "Title")[1]
description <- gsub("\n"," ",read.dcf("DESCRIPTION", fields = "Description")[1])
URL <- read.dcf('DESCRIPTION', fields = 'URL')[1]
owner <- strsplit(URL,"/")[[1]][4]
repo <-strsplit(URL,"/")[[1]][5]
```
## Introduction
Many genes have been associated with diseases
Multi-Scale Target Explorer (`MSTExplorer`) systematically identifies, prioritises, and visualises cell-type-specific gene therapy targets across the phenome.
Core functionalities include:
**1. Conducting phenotype x cell type genetic association tests at scale**
- 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/)).
- Whole-body scRNA-seq atlases from humans (across multiple developmental stages) are used as a data-driven source of cell type-specific gene markers.
- 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 >11k phenotypes x >200 cell types (>2,200,000 associations) can be in <30 minutes on a Macbook laptop with 10 CPU cores).
**2. Inferring multi-scale causal graphs of disease**
`MSTExplorer` allows users to easily infer and construct multi-scale causal graphs of Diseases (blue nodes) -> Phenotypes (purple nodes) -> Cell types (orange nodes) -> Genes (yellow nodes).
{height=400px}
[See here for more example networks.](https://github.com/neurogenomics/rare_disease_celltyping/tree/299abe0ccd00644bc2f05a1389704fe196a3e868/manuscript/_manuscript/img/fig-therapy-examples-supp).
**3. Prioritising cell-type-specific gene therapy targets**
`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.
## Installation
Within R:
```R
if(!require("BiocManager")) install.packages("BiocManager")
BiocManager::install("`r paste(owner,repo,sep='/')`")
library(`r pkg`)
```
## Documentation
#### [Website](https://`r owner`.github.io/`r pkg`)
#### [Get started](https://`r owner`.github.io/`r pkg`/articles/`r pkg`)
#### [Docker/Singularity Container](https://`r owner`.github.io/`r pkg`/articles/docker.html)
## Citation
If you use ``r pkg``, please cite:
> `r utils::citation(pkg)$textVersion`
## Contact
### [Neurogenomics Lab](https://www.neurogenomics.co.uk)
UK Dementia Research Institute
Department of Brain Sciences
Faculty of Medicine
Imperial College London
[GitHub](https://github.com/neurogenomics)
## Session Info
```{r Session Info}
utils::sessionInfo()
```