---
title: "Overview"
author: "Martin Morgan (martin.morgan@roswellpark.org)<br />
    Roswell Park Cancer Institute, Buffalo, NY<br />
    5 - 9 October, 2015"
output:
  BiocStyle::html_document:
    toc: true
    toc_depth: 2
vignette: >
  % \VignetteIndexEntry{Overview}
  % \VignetteEngine{knitr::rmarkdown}
---

```{r style, echo = FALSE, results = 'asis'}
BiocStyle::markdown()
options(width=100, max.print=1000)
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")))
```

The material in my parts of the course requires _R_ version 3.2 and
_Bioconductor_ version 3.2

```{r configure-test}
stopifnot(
    getRversion() >= '3.2' && getRversion() < '3.3',
    BiocInstaller::biocVersion() == "3.2"
)
```

1. [Introduction to R / Bioconductor](V1-Introduction.html) (T)
2. [Working with Data: `SummarizedExperiment`](V2-WorkingWithData.html) (P)
3. [Genomic Ranges and other Data Structures For Genome-Scale Data And Annotation](V3-GenomicRanges.html) (P)
4. [Adding Annotation To Your Analysis](V4-Annotation.html) (P)
5. [Counting Reads And Working With Large Files](V5-LargeFiles.html) (P)
6. [RNA-Seq Differential Expression](V6-RNASeq.html) (P)
7. [ChIP-Seq For Understanding Gene Regulation](V7-ChIPSeq.html) (P)
8. [Motifs](V8-Motifs.html) (P)
9. [Visualizing Genomic Data](V9-Visualization.html) (P)

(T): Talk; (P): Practical.