* [R / Bioconductor Packages for Short Read Analysis](BioconductorIntroduction.pdf)
* [Short Read Alignment](rna_seq.pdf)
* [ShortRead and Rsamtools for Input and Quality Assessment](ShortRead.pdf)
* [IRanges, GenomicRanges, and Biostrings](GenomicRanges.pdf)
* [GenomicFeatures and BSgenome](GenomicFeatures.pdf)
* [Differential expression analysis for sequencing count data](DESeq.pdf)
* [ChIP-seq data analysis with SWEMBL](Chip-seq.SWEMBL.pdf)
* [MACS, CisGenome, SISSRs and other peak calling algorithms](
  ChipSeq_June2010_Peak_Disco_public-version.pdf)
* [Sensitivity, Specificity, ROC, Multiple testing, and Independent filtering](
  100609-multtestindepfilt-huber.pdf)
* [Hilbert curves](100609-hilbertcurve-huber.pdf)
* [Practical 1: Reading and Manipulating Short Reads](Practical-1-ShortRead.pdf)
* [Practical 3: A ChIP-Seq Workflow](Practical-3-ChIPSeq.pdf)
* [Practical 4: Finding Structural Variants in Short Read, Paired-end Sequence
  Data with R and Bioconductor](Practical-4-StructuralVariants.pdf)
* [EMBL2010_0.0.11.tar.gz package](EMBL2010_0.0.11.tar.gz) - An R package
  containing slides and exercise material. Download, then install in R using
  `install.packages("EMBL2010_0.0.11.tar.gz", repos=NULL, type="source")`