<!--
%\VignetteIndexEntry{01. Use R / Bioconductor for Sequence Analysis}
%\VignettePackage{UseBioconductor}
%\VignetteEngine{knitr::knitr}
-->

```{r setup, echo=FALSE}
library(UseBioconductor)
stopifnot(BiocInstaller::biocVersion() == "3.1")
```

```{r style, echo = FALSE, results = 'asis'}
BiocStyle::markdown()
```

# Use R / Bioconductor for Sequence Analysis

This package contains training material for a Winter, 2014
intermediate _R_ / _Bioconductor_ course "Use _R_ / _Bioconductor_ for
Sequence Analysis", offered February 4, Genentech, San Francisco, CA.

This course is directed at intermediate users wanting to make
effective use of _R_ and _[Bioconductor](http://bioconductor.org)_ for
the analysis and comprehension of high-throughput sequence data. The
morning provides overall orientation to the packages and facilities
available in _Bioconductor_, including and in-depth look at the
central _GenomicRanges_ infrastructure. The afternoon provides
approaches to common challenges -- working with large data, placing
statistical results in biological context, and effectively and
reliably communicating results with other team members.  

The course combines lectures with extensive hands-on practicals;
participants are required to bring a laptop with wireless internet
access and a modern version of the Chrome or Safari web browser.

## Schedule (tentative)

Use _R_ / _Bioconductor_

- 9:00 - 10:00
  [Introduction to _Bioconductor_](A01.1_IntroductionToBioconductor.html):
  package and class infrastructure in the high-throughput sequencing
  landscape
- 10:00 - 11:45 [GenomicRanges](A01.2_GenomicRanges.html)
  design and use for data and annotation 
- 11:45 - 12:30 A high-level tour of
  [new and relevant packages](A01.3_NewPackages.html)
- 1:30 - 2:30 [Working with large data](A01.4_LargeData.html) and
  collections of genomic files.
- 2:30 - 3:30 Package, web, and cloud-based
  [annotation resources](A01.5_Annotation.html), including use of data
  base and web service resources
- 3:45 - 4:45 Genome-specific
  [visualization and reports](A01.6_Shiny.html), including
  interactivity
- 4:45 - 5:00 Summary
