Course Agenda

Sunday, June 22
17:00 - 18:00Installation Help Desk
18:00 - 20:30 Get Together with drinks and nibbles
Monday, June 23
8:30-9:15 Lecture 01Introduction to R and Bioconductor (MM)
9:15-10:00 Lecture 02Basics of high-throughput sequencing technologies and short read aligners (SA)
10:30-11:15Lecture 03Elements of statistics 1: t-test and linear model (RG)
11:15-11:20Overview over the afternoon labs
11:20-12:00Lecture 04Elements of statistics 2: multiple testing, false discovery rates, independent filtering (WH)
12:00-13:00Break(lunch self-organised)
13:00-14:00 Installation help desk
14:00-17:00TutorialR introduction/refresher: data types, reading and writing files and spreadsheets, plotting, programming, functions and packages. (LG) - alternatively: -
14:00-17:00Lab 1Exploratory data analysis and visualization (VJC)
Lab 2Intermediate R 1: Skills for Intermediate R Users: classes, methods, packages, and scalable computing (ML, MM)
Lab 3Intermediate R 2: Scalable genomics (ML, MM)
15:15-15:30Coffee Break
17:00-18:30Prosecco & Posters
Tuesday, June 24
8:30-9:15 Lecture 05RNA-Seq 1: differential expression analysis - GLMs and testing (SA)
9:15-10:00 Lecture 06RNA-Seq 2: shrinkage, empirical Bayes, FC estimation (SA)
10:30-11:15Lecture 07Visualisation (VJC)
11:15-12:00Lecture 08Computing with genomic ranges, sequences and alignments (MM)
12:00-14:00Break(lunch self-organised)
14:00-17:00Lab 4A complete RNA-Seq differential expression workflow (WH, SA, AR): start from FASTQ files, align to genome, summarizeOverlaps, DESeq2, basic gene set enrichment, exon-level analysis
15:15-15:30Coffee Break
Wednesday, June 25
8:30-9:15 Lecture 09DNA-Seq 1: Variant calling (ML)
9:15-10:00 Lecture 10DNA-Seq2: visualisation and quality assessment of variant calls (PP)
10:30-11:15Lecture 11Gene set enrichment analysis (RG)
11:15-12:00Lecture 12Leveraging annotation and data integration: working with gene and genome annotations (MM)
12:00-14:00Break(lunch self-organised)
14:00-22:00Social programmeExcursion to the mountains, dinner
Thursday, June 26
8:30-9:15 Lecture 13RNA-Seq 3: alternative exon usage (AR, with SA & WH, ML)
9:15-10:00 Lecture 14Elements of statistics 3: Classification and clustering - basic concepts (VJC)
10:30-11:15Lecture 15Elements of statistics 4: regularisation & kernels (WH)
11:15-12:00Lecture 16ChIP-Seq (ML)
12:00-14:00Break(lunch self-organised)
14:00-15:15Lab 5Working with the Ranges infrastructure: annotating and understanding regions ("what to do downstream of a ChIP-Seq analysis or DNA-variant calling experiment?") (MM)
15:15-15:30Coffee Break
15:30-17:00Lab 6Tallies, visualisation, HDF5 (PP, with WH)
Friday, June 27
8:30-9:15 Lecture 17Elements of statistics 5: experimental design (SA, WH)
9:15-10:00 Lecture 18 eQTL / molecular-QTL analyses (VJC)
10:30-11:15Lecture 19Proteomics (LG)
11:15-12:00Lecture 20Emerging topic
12:00-14:00Break(lunch self-organised)
14:00-15:15Lab 7Reporting your analysis - authoring knitr/Rmarkdown, ReportingTools, shiny (LG)
15:15-15:30Coffee Break
15:30-17:00Labs 1-7Continue & finish all labs
Lecturers and TAs
Robert Gentleman (RG), Martin Morgan (MM), Vincent Carey (VJC), Michael Lawrence (ML), Wolfgang Huber (WH), Simon Anders (SA), Laurent Gatto (LG), Alejandro Reyes (AR), Paul Pyl (PP), Andrzej Oles (AO), Malgorzata Oles (MO)