```{r setup, echo=FALSE} library(LearnBioconductor) stopifnot(BiocInstaller::biocVersion() == "3.1") ``` ```{r style, echo = FALSE, results = 'asis'} BiocStyle::markdown() ``` # Learning R / Bioconductor for Sequence Analysis This package contains training material for a Winter, 2014 introductory _R_ / _Bioconductor_ course "Learning _R_ / _Bioconductor_ for Sequence Analysis", offered February 2-3, Genentech, San Francisco, CA. This course is directed at beginning and intermediate users who would like an introduction to the analysis and comprehension of high-throughput sequence data using _R_ and _[Bioconductor](http://bioconductor.org)_. Day 1 focuses on learning essential background: an introduction to the _R_ programming language; central concepts for effective use of _Bioconductor_ software; and an overview of high-throughput sequence analysis work flows. The morning of Day 2 emphasizes use of _Bioconductor_ for specific tasks, and in particular takes detailed look at RNA-seq differential expression work flow. The afternoon of Day 2 transitions to understanding effective approaches for managing larger challenges: strategies for working with large data, writing re-usable functions, developing reproducible reports and work flows, and visualizing results. 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) Day 1: Learn _R_ / _Bioconductor_ - 9:00 - 10:30 [Introduction to _R_](A01.1_IntroductionToR.html): objects, functions, help! - 11:00 - 12:30 [Introduction to _Bioconductor_](A01.2_IntroductionToBioconductor.html): working with packages and classes - 1:30 - 5:00 (break: 3:00 - 3:30) [Introduction to sequence analysis](A01.3_BioconductorForSequenceAnalysis.html): typical work flow; data types and quality assessment; essential _Bioconductor_ packages Day 2: Use _R_ / _Bioconductor_ - 9:00 - 12:00 (break: 10:30 - 11:00) An RNA-seq differential expression work flow ([lecture](B02.1_RNASeq.html); [practical](B02.1.1_RNASeqLab.html)) - 12:00 - 12:30 [Other work flows](B02.2_CommonWorkFlows.html) (survey): ChIP-seq, variants, copy number, epigenomics - 1:30 - 2:15 [Working with large data](C03.1_LargeData.html) - 2:15 - 3:00 [Organizing code in functions, files, and packages](C03.2_CodeToPackages.html) - 3:15 - 4:00 [Reproducible reports and work flows](C03.3_ReproducibleResearch.html) - 4:00 - 4:45 [Visualization](C03.4_Visualization.html) - 4:45 - 5:00 Summary