This is a collection of repositories from the Cardiovascular Genomics and Precision Medicine team at Imperial College London
The Cardiovascular Genomics and Precision Medicine group (Ware lab) spans the National Heart & Lung Institute at Imperial College London, the MRC Laboratory of Medical Sciences (LMS), Imperial College Healthcare NHS Trust, and the Royal Brompton & Harefield Hospitals group at Guy's and St Thomas' Hospitals NHS Trust.
Web resources from the group
cvgenetics.org has information about the group and an index of our published resources
cardiodb.org hosts our webtools
James' personal web page at Imperial College
The group web page at MRC LMS
Selected public repositories
| Public repos supporting published work: | PMC ID / DOI | Description |
|---|---|---|
| ACM | PMC5957753 | Genetic Etiology for Alcohol-Induced Cardiac Toxicity |
| CardioBoost_manuscript | PMC7790749 | AI Missense Variant Pathogenicity Prediction for Inherited Cardiac Conditions |
| CardioClassifierManuscript | PMC6558251 | CardioClassifier decision support tool for ICC variant interpretation in ACMG framework |
| frequencyFilter | PMC5563454 | Framework to use variant frequency data in clinical genome intepretation |
| homologous-missense-constraint | medRxiv | Estimating genetic constraint at single amino acid resolution using homologous protein domain structures |
| ResponseToShahEtAl | https://doi.org/10.1016/j.gim.2021.10.020 | A response to updated ACMG secondary findings guidelines that recommend returning SFs in cardiomyopathy genes including Titin |
| uORFs | PMC7253449 | Characterising the loss-of-function impact of 5’ untranslated region variants in gnomAD |
| UTRannotator | PMC8150139 | A VEP plug-in to annotate UTR variants |
| ParalogueAnnotator | pending | A VEP plug-in to perform paralogue annotation |
| ParalogueAnnotation_personal | bioRxiv | manuscript validating utility of paralogue annotation for missense variant interpretation |
| Paralogue_Annotation_App | bioRxiv | codebase for the paralogue annotation web app |
| G2P-Cardiac-Panel | PMC10594882 | CardiacG2P is an evidence-based dataset for inherited cardiac condition gene disease pairs |
| Other public repos: | |
|---|---|
| BioinfoJournalClub | |
| cTTN | |
| gnomadjs | |
| variantfx | |
| web |
| Repos on James' github: | description | PMCID / DOI |
|---|---|---|
| alleleFrequencyApp | PMC5563454 | |
| denovolyzeR | An R package for statistical analyses of de novo genetic variants | |
| denovolyzeR.org | Code for the denovolyeR website | denovolyzer.org |
| denovolyzerManuscript | Current protocols in human genetics denovolyzeR manuscript (manuscript source code) | |
| denovolyzeR-ProbabilityTables | Additional probability tables to be used with denovolyzeR | NA |
| eLife_Alamo2017 | Code to reproduce analyses presented in Alamo et al, eLife 2017 | |
| APPRAISE | A Bayesian framework for the analysis and interpretation of rare genetic variants | PMC / URL |
| knitauthors | An unpublished R package to format & number author/affiliation lists for publication | |
| reproSci / demo | Code for teaching / demonstrating RMarkdown, including manuscript preparation | |
Selected private repositories
An index and overview of key internal resources is maintained at https://github.com/ImperialCardioGenetics/private-github-index (accessible to team members only)