• R / Bioconductor Packages for Short Read Analysis
• Short Read Alignment
• ShortRead and Rsamtools for Input and Quality Assessment
• IRanges, GenomicRanges, and Biostrings
• GenomicFeatures and BSgenome
• Differential expression analysis for sequencing count data
• ChIP-seq data analysis with SWEMBL
• MACS, CisGenome, SISSRs and other peak calling algorithms
• Sensitivity, Specificity, ROC, Multiple testing, and Independent filtering
• Hilbert curves
• Practical 1: Reading and Manipulating Short Reads
• Practical 3: A ChIP-Seq Workflow
• Practical 4: Finding Structural Variants in Short Read, Paired-end Sequence Data with R and Bioconductor
• EMBL2010_0.0.11.tar.gz package - 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")