---
title: 'bigPint Vignette'
author:
- name: Lindsay Rutter
date: '`r Sys.Date()`'
package: bigPint
bibliography: bigPint.bib
output:
    BiocStyle::html_document:
    toc_float: true
    tidy: TRUE
vignette: >
    \usepackage[utf8]{inputenc}
    %\VignetteIndexEntry{"bigPint Vignette"}
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}
    %\VignettePackage{bigPint}
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo=TRUE)
```

## Accessing the vignette

Welcome to the `bigPint` package! If you are a new user, please visit the 
package website at [https://lindsayrutter.github.io/bigPint/](https://lindsayrutter.github.io/bigPint/). There, you will find a general overview of the `bigPint` package 
and the motivations behind it. You will also find ten short vignette articles 
that we recommend reading in order. These short vignette articles consist of 
reproducible code that provide:

- An introduction to `bigPint` plots and how to interpret them
- A guide to installing the `bigPint` package
- Expected formats of two input objects in most `bigPint` functions
- How to produce static `bigPint` plots
- How to produce interactive `bigPint` plots
- How to perform hierarchical clustering and use the clusters in `bigPint` 
    functions
- A recommended RNA-seq visualization pipeline with example code for you to 
    follow

