index.Rmd

---
title: "About"
description: |
  We investigated the differential effects of *APOE* alleles on the microglia and astrocyte transcriptome in the absence and presence of neuritic plaques (NPs) using bulk brain RNA-seq data from two large brain banks and performed follow-on experiments in *APOE* knock-in mice.
site: distill::distill_website
output:
  distill::distill_article:
    toc: true
---

```{r include = FALSE, eval = FALSE}

# to render website
library(rmarkdown)
library(distill)
render_site()

# to remove files
clean_site()

```

# Setup
Install [R](https://www.r-project.org/) to run our code.

# Documentation
To read our documented code, please visit [mindds.github.io/apoe-glia](https://mindds.github.io/apoe-glia) or see below.

### Functions
* [Models](https://mindds.github.io/apoe-glia/models)
* [Spectral Clustering](https://mindds.github.io/apoe-glia/spectral-clustering)

### ROSMAP
* [Define Variables](https://mindds.github.io/apoe-glia/ROSMAP-variables)
* [Pre-Process Data](https://mindds.github.io/apoe-glia/ROSMAP-preprocess)
* [Microglia Analysis](https://mindds.github.io/apoe-glia/ROSMAP-microglia)
* [Astrocyte Analysis](https://mindds.github.io/apoe-glia/ROSMAP-astrocyte)

### MSBB
* [Define Variables](https://mindds.github.io/apoe-glia/MSBB-variables)
* [Merge Data](https://mindds.github.io/apoe-glia/MSBB-merge)
* [Microglia Analysis](https://mindds.github.io/apoe-glia/MSBB-microglia)

### qPCR Analysis
* [qPCR Analysis](https://mindds.github.io/apoe-glia/qPCR-analysis)

# Code Availability
Our full codebase is available for download on [GitHub](https://github.com/mindds/apoe-glia).