---
title: "systemPipeR: Workflow Templates" 
author: "Author: Le Zhang, Daniela Cassol, and Thomas Girke"
date: "Last update: `r format(Sys.time(), '%d %B, %Y')`" 
output:
  BiocStyle::html_document:
    toc_float: true
    code_folding: show
  BiocStyle::pdf_document: default
package: systemPipeR
vignette: |
  %\VignetteEncoding{UTF-8}
  %\VignetteIndexEntry{systemPipeR: Workflow Templates}
  %\VignetteEngine{knitr::rmarkdown}
fontsize: 14pt
bibliography: bibtex.bib
---

<!--
- Compile from command-line
Rscript -e "rmarkdown::render('systemPipeR_workflows.Rmd', c('BiocStyle::html_document'), clean=F); knitr::knit('systemPipeR_workflows.Rmd', tangle=FALSE)"
-->

```{css, echo=FALSE}
pre code {
white-space: pre !important;
overflow-x: scroll !important;
word-break: keep-all !important;
word-wrap: initial !important;
}
```

```{r style, echo = FALSE, results = 'asis'}
BiocStyle::markdown()
options(width=80, max.print=1000)
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")), 
    tidy.opts=list(width.cutoff=80), tidy=TRUE)
```

```{r setup, echo=FALSE, messages=FALSE, warnings=FALSE}
suppressPackageStartupMessages({
    library(systemPipeR)
})
```

# Redirect notification

The
[systemPipeRdata](https://www.bioconductor.org/packages/devel/data/experiment/html/systemPipeRdata.html)
package provides a collection of pre-built workflow templates that are ready to
use from
[systemPipeR](https://www.bioconductor.org/packages/devel/bioc/html/systemPipeR.html).
These templates are described in detail in the associated `systemPipeRdata`
overview vignette
[here](https://www.bioconductor.org/packages/devel/data/experiment/vignettes/systemPipeRdata/inst/doc/systemPipeRdata.html),
which includes instructions on how to use them.


# Funding

This project is funded by awards from the National Science Foundation ([ABI-1661152](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1661152)], 
and the National Institute on Aging of the National Institutes of Health ([U19AG023122](https://reporter.nih.gov/project-details/9632486)).