https://github.com/imperialcollegelondon/fractalgenetics
Analysis of the genomic architecture and functional role of myocardial trabeculae
Science Score: 46.0%
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Low similarity (10.3%) to scientific vocabulary
Repository
Analysis of the genomic architecture and functional role of myocardial trabeculae
Basic Info
- Host: GitHub
- Owner: ImperialCollegeLondon
- Language: MATLAB
- Default Branch: master
- Size: 34.6 MB
Statistics
- Stars: 13
- Watchers: 5
- Forks: 5
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Genetic and functional insights into the fractal structure of the heart
The endocardial surface of the adult human hearts consists of a complex network of muscular trabeculae. Thought to be a remnant of embryonic development, it remains uknown why these complex structures still persistent in the adult organ. Here, we use population genomics, image-based intermediate phenotyping and in silico modelling to determine the effect of this complex cardiovascular trait on function.
The following repository contains all data analysis and processing scripts applied in the study.
Software requirements
Data processing and analysis is embedded into different snakemake (v5.1.5) workflows. Genetics analyses require plink v1.9 and v2 as well as flashpca. Data visualisation and processing is done in R, version 3.6.1. Genetic association testing requires Bgenie v1.3. Fractal analysis requires Matlab, MATLAB Compiler Runtime (MCR) 2016b and Ghostscript. Finite element modeling was conducted with Abaqus/Standard, Simulia.
Content
1. Automated-fractal-analysis
Automated fractal analysis of segmented cardiac images using pre-exisiting image segmentations to determine a region of interest within the myocardium.
2. Fractal-analysis-processing
Code for post-processing of fractal-analysis results including interpolation of FD values to a common number of slices across individuals, summary statistics of FD values per individual and a collection of functions for co-registration of myocardial and trabeculation outlines.
3. UK-Biobank
Trabeculation GWAS in UK Biobank containing analysis pipelines for genotype and phenotype processing, GWAS, GWAS results processing, functional enrichement, Mendelian randomisation analyses and LDhub analyses in discovery and replication study.
4. UK Digital Heart Project
Trabeculation GWAS in the UK Digital Heart Project cohort (second replication cohort) containing analysis pipelines for genotype and phenotype processing, GWAS and GWAS results processing.
5. Finite element modelling
Finite element modeling input files (Abaqus Standard, SIMULIA, Dessault Systemes)for the simulation of 5 consecutive cardiac cycles of the left ventricle, starting from the ventricular reference configuration (zero ventricular pressure).
Citation
Meyer HV et al., Genetic and functional insights into the fractal structure of the heart, Nature, 2020, DOI:10.1038/s41586-020-2635-8
See
McGurk KA et al., https://github.com/ImperialCollegeLondon/trabecular_variants
Owner
- Name: Imperial College London
- Login: ImperialCollegeLondon
- Kind: organization
- Email: icgithub-support@imperial.ac.uk
- Location: Imperial College London
- Repositories: 311
- Profile: https://github.com/ImperialCollegeLondon
Imperial College main code repository
GitHub Events
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Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Hannah | h****r@g****m | 246 |
| Declan O'Regan | d****n@i****k | 61 |
| HannahVMeyer | h****r@g****m | 58 |
| ptokarcz | 3****z | 38 |
| HannahVMeyer | H****r | 21 |
| Tim Dawes | t****s@i****k | 20 |
| Kathryn McGurk | 5****k | 14 |
| Jiashen Cai | c****n@g****m | 14 |
| marta-serrani | 4****i | 2 |
| Hannah Meyer | h****h@e****k | 1 |
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