Monday, June 22

Morning talks

• pdf Introduction to R and Bioconductor
• pdf Basics of high-throughput sequencing technologies and short read aligners
• pdf Elements of statistics 1: t-test and linear model
• pdf Elements of statistics 2: multiple testing, false discovery rates, independent filtering

Afternoon labs

• zip R introduction/refresher: data types, reading and writing files and spreadsheets, plotting, programming, functions and packages.

• pdf R Exploratory data analysis and visualization (pdf solutions)

• html R Intermediate R 1: accessing resources - packages, classes, methods, and efficient code. Download IntermediateR1_1.0.0.tar.gz and install as:

  source("http://bioconductor.org/biocLite.R")
  biocLite(c("IRanges", "GenomicRanges", "microbenchmark"))
  install.packages("IntermediateR1_1.0.0.tar.gz", repos=NULL, type="source")
  

• pdf R Intermediate R 2: scalable / performant computing. (Large files needed for some of this lab are NOT available for download). Download CSAMA2014ScalableComputingLab_0.0.1.tar.gz and install as:

  source("http://bioconductor.org/biocLite.R")
  biocLite(c("IRanges", "GenomicRanges", "Rsamtools", "ShortRead", 
      "rtracklayer", "GenomicAlignments", "GEOquery", "microbenchmark",
      "BiocParallel", "ggbio", "Biobase", "GenomicFiles"))
  install.packages("CSAMA2014ScalableComputingLab_0.0.1.tar.gz",
      repos=NULL, type="source")
  

Tuesday

Morning talks

• pdf RNA-Seq 1: differential expression analysis - GLMs and testing
• RNA-Seq 2: shrinkage, empirical Bayes, FC estimation
• pdf Visualisation
• pdf Computing with genomic ranges, sequences and alignments

Afternoon labs

• pdf R (Rnw, bib) A complete RNA-Seq differential expression workflow DESeq2_result_table.RData Homo_sapiens.GRCh37.75.subset.gtf.gz

Wednesday

Morning talks

• pdf DNA-Seq 1: Variant calling
• pdf DNA-Seq 2: visualisation and quality assessment of variant calls
• pdf Gene set enrichment analysis
• pdf R Working with gene and genome annotations

Afternoon labs

• pdf R Variant tallies, visualisation, HDF5 ExampleData.zip NRAS.tally.hfs5

Thursday

Morning talks

• pdf RNA-Seq 3: alternative exon usage
• html Elements of statistics 3: Classification and clustering - basic concepts
• pdf Elements of statistics 4: regularisation & kernels
• pdf R ChIP-Seq

Afternoon labs

• pdf R Working with the Ranges infrastructure: annotating and understanding regions

Friday

Morning talks

• pdf Elements of statistics 5: experimental design
• pdf eQTL / molecular-QTL analyses
• pdf Proteomics
• Emerging topic -- pdf image analysis

Afternoon labs

• Reporting your analysis - authoring knitr/Rmarkdown, ReportingTools, shiny. rauthoring_0.2.2.tar.gz