swvanderlaan/gbastoolkit

A ToolKit to perform gene-based association studies using VEGAS or MAGMA

Hi there 👋

✨ I am a biologist turned geneticist and bioinformatician interested in medical problems with a passion for ✨ OpenScience ✨

🔭 My research interest is focused on the genetic causes of atherosclerosis underlying cardiovascular diseases. With my work I ultimately aim to move from genetic loci identified in large-scale genome-wide association studies to novel therapeutic targets and (surrogate) biomarkers for atherosclerotic diseases through extensive in silico, and in vitro modelling.

👯 I’m always happy to collaborate on any subject mixing cardiovascular diseases with genetics.

💬 Ask me anything about James Bond.

📫 Follow me @swvanderlaan.

⚡ Fun fact: I once dyed my hair blond and worked at a start-up biotech ...

^{Copyright since 1979 | Sander W. van der Laan | vanderlaanand.science.}

gbastoolkit's Issues

GBASToolKit: add in VEGAS2 GSEA

Add in VEGAS2 based pathway enrichment analysis 🚧

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Reference: resource creator

Add in download and parsing script for reference to enable per-chromosome analyses 🔷

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Reference: add in legacy HapMap2 (VEGAS2 only)

Add in HapMap2 as reference (VEGAS2 only) 🔷

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Installation: dependency check

Add script to check for dependencies 🔶

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Resource: resource creator for non-genes

Extent resource script with download of functional elements, to facilitate the analysis of transcription binding sites, or active enhancers, etc. 🔶

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Installation: workflow for installing PLINK2, VEGAS2, and MAGMA

Workflows for installing PLINK2, VEGAS2 and MAGMA properly 🔷

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Plotting: Manhattan plotting

Add (option) to plot results in a Manhattan 🔶

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☑️ implemented
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Plotting: add gene-names to Manhattan

Add gene-names based on a threshold to Manhattan 🔷

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☑️ implemented
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Plotting: regional association plotting

Add option to plot regional plots of significant genes 🔷

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☑️ implemented
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All issues

Things to do for future versions

☑️ implemented
❌ skipped
🚧 working on it
🔶 next version, high priority
🔷 next version, low priority

Scripts

• add script to check for dependencies 🔶
• workflows for installing PLINK2, VEGAS2 and MAGMA properly 🔷
• add in HapMap2 as reference (VEGAS2 only) 🔷
• add in download and parsing script for reference to enable per-chromosome analyses 🔷
• add in VEGAS2 based pathway enrichment analysis 🚧
• extent resource script with download of functional elements, to facilitate the analysis of transcription binding sites, or active enhancers, etc. 🔶

Plotting

• add (option) to plot results in a Manhattan 🔶
• add (option) to plot results in a QQ-plot 🔶
• add gene-names based on a threshold to Manhattan 🔷
• add option to plot regional plots of significant genes 🔷

Plotting: QQ-plot

Add (option) to plot results in a QQ-plot 🔶

Legend

☑️ implemented
❌ skipped
🚧 working on it
🔶 next version, high priority
🔷 next version, low priority