index.Rmd

---
title: "Gene-vegetarianism interactions"
author: Mike Francis
date: "`r Sys.time()`"
output:
  html_document:
    toc: false
    includes:
      in_header: "favicon.html"
---

### ![](images/paste-C5ECBF03.png)

### Here, you will find the code used in the manuscript, "**Gene-vegetarianism interactions detected in genome-wide analyses across 30 serum biomarkers**"<br/><br/>

### Our goal in this website was to make the analysis in our study as transparent and helpful as possible.<br/><br/>

### Please feel free to use our code and cite our paper!<br/>

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## Site highlights:

#### **· [Defining vegetarians](https://michaelofrancis.github.io/VegetarianGDI/DefineVeg.html)**

#### **· [Matching and effects analysis](https://michaelofrancis.github.io/VegetarianGDI/MatchEffect.html)**

#### **· [Interactive Manhattan plots](https://michaelofrancis.github.io/VegetarianGDI/GxEplots.html)**

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## Download summary statistics

<br/>

#### GWAS and GWIS summary statistics are hosted by GWAS Catalog.

#### They can be downloaded using the accessions found in this table:<br/>

```{r, echo=FALSE}
library(fontawesome)
library(downloadthis)
download_link(
  link = "https://github.com/michaelofrancis/VegetarianGDI/blob/main/Gene-Veg_GWASCatalog_Accessions.xlsx?raw=true",
  button_label = "Download sumstats accessions table",
  button_type = "primary",
  has_icon = TRUE,
  icon = "fa fa-save",
  self_contained = TRUE
)
```

<br/><br/>

#### Download gene-level summary statistics (MAGMA output): <br/>

```{r, echo=FALSE}

download_link(
  link = "https://github.com/michaelofrancis/VegetarianGDI/blob/main/GenexVegetarian-MAGMA-sumstats.zip?raw=true",
  button_label = "Download gene-level sumstats",
  button_type = "primary",
  has_icon = TRUE,
  icon = "fa fa-save",
  self_contained = TRUE
)
```

<br/>

------------------------------------------------------------------------

<br/><br/>

#### Download Supplementary Figures: <br/>

```{r, echo=FALSE}

download_link(
  link = "https://github.com/michaelofrancis/VegetarianGDI/blob/main/SupplementaryFigures.pdf?raw=true",
  button_label = "Download Supplementary Figures 1-10",
  button_type = "danger",
  has_icon = TRUE,
  icon = "fa fa-save",
  self_contained = TRUE
)
```

<br/>

------------------------------------------------------------------------

#### Questions about this study or this website? Contact Michael Francis at michaelfrancisphd\@protonmail.com

#### Github repository for this website is [here](https://github.com/michaelofrancis/VegetarianGDI)