```{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