https://github.com/mmkim1210/geneticsmakie.jl

🧬High-performance genetics- and genomics-related data visualization using Makie.jl
https://github.com/mmkim1210/geneticsmakie.jl

bioinformatics cairomakie colocalization data-science fine-mapping genetics genomics gwas julia julia-language linkage locuszoom makie multi-ethnic multivariate openmendel phewas qtl v2f visualization

Last synced: about 1 month ago
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🧬High-performance genetics- and genomics-related data visualization using Makie.jl

• Host: GitHub
• URL: https://github.com/mmkim1210/geneticsmakie.jl
• Owner: mmkim1210
• License: mit
• Created: 2021-11-28T06:45:49.000Z (almost 3 years ago)
• Default Branch: master
• Last Pushed: 2024-06-15T04:46:31.000Z (5 months ago)
• Last Synced: 2024-10-12T23:21:50.490Z (about 1 month ago)
• Topics: bioinformatics, cairomakie, colocalization, data-science, fine-mapping, genetics, genomics, gwas, julia, julia-language, linkage, locuszoom, makie, multi-ethnic, multivariate, openmendel, phewas, qtl, v2f, visualization
• Language: Julia
• Homepage: https://mmkim1210.github.io/GeneticsMakie.jl/dev/
• Size: 30.5 MB
• Stars: 82
• Watchers: 4
• Forks: 2
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        


# GeneticsMakie

[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://mmkim1210.github.io/GeneticsMakie.jl/dev)

[![Build Status](https://github.com/mmkim1210/GeneticsMakie.jl/workflows/CI/badge.svg)](https://github.com/mmkim1210/GeneticsMakie.jl/actions)

[![Coverage](https://codecov.io/gh/mmkim1210/GeneticsMakie.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/mmkim1210/GeneticsMakie.jl)

[![Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/GeneticsMakie&label=downloads)](https://pkgs.genieframework.com/?packages=GeneticsMakie)

## Installation

GeneticsMakie.jl supports  Julia  v1.6 or later.

```julia

julia> ]

pkg> add GeneticsMakie

```

## Documentation

[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://mmkim1210.github.io/GeneticsMakie.jl/dev)

## Examples

Visualize 1 Mb window around *KMT2E* gene:



Highlight *KMT2E* gene and several nearby genes:



Visualize *KMT2E* isoforms:



Visualize *KMT2E* and nearby isoforms simultaneously:



Visualize *KMT2E* isoforms w/ randomly generated expression



Visualize LD for *KMT2E* locus:



Visualize LD as a square for *KMT2E* locus:



Visualize GWAS results for *KMT2E* locus:



Visualize GWAS results for *KMT2E* locus with the same reference SNPs for LD:



Visualize Manhattan plot:



Visualize Miami/Hudson plot:



Visualize QQ plot of *P* values:



## Further examples

Patterns of association and LD:



Colocalization of GWAS signals:



Association results across multiple phenotypes:



MHC association for schizophrenia with increasing sample size:





LD structure for ~66,000 SNPs in MHC region:



## References

> Kim et al., (2022). GeneticsMakie.jl: A versatile and scalable toolkit for visualizing locus-level genetic and genomic data. *Bioinformatics*, https://doi.org/10.1093/bioinformatics/btac786.