Programme

Sunday, June 14

17:00–18:00 Registration & Installation help desk
18:00–20:00 Get Together with drinks and nibbles

Monday, June 15

08:30–09:15 Lecture 01 Introduction to R and Bioconductor (MM)
09:15–10:00 Lecture 02 Basics of sequence alignment and aligners (SA)
10:00–10:30 Coffee break
10:30–11:15 Lecture 03a Hypothesis testing and multiple testing (WH)
11:15–12:00 Lecture 04 Clustering and classification (VJC)
12:00–13:00 Lunch break (self-organised)
13:00–14:00 Installation help desk
14:00–15:30 Lab 1 Introduction to Bioconductor (MM)
15:30–17:00 Lab 2 Reproducible research and R authoring with markdown and knitr (LG)
17:00–17:30 Flashlight talks

  • Amit Blumberg
  • Daniele Capocefalo
  • Sulev Koks
  • Vang Le

Tuesday, June 16

08:30–09:15 Lecture 05 RNA-Seq data analysis and differential expression part I (SA)
09:15–10:00 Lecture 06 RNA-Seq data analysis and differential expression part II (ML)
10:00–10:30 Coffee break
10:30–11:15 Lecture 07 Computing with sequences and genomic intervals (MM)
11:15–12:00 Lecture 08 Epigenetics and ChIP-Seq (AP)
12:00–14:00 Lunch break (self-organised)
14:00–17:00 Lab 3 End-to-end RNA-Seq workflow (ML, SA)
17:00–17:30 Flashlight talks

  • Soledad Gomez Gonzales
  • Michal Lipinski
  • Thale Kristin Olsen
  • Luis M. Valor

Wednesday, June 17

08:30–10:00 Lecture 09 Working with DNA Variant calls – QA/QC, visualization, annotation and integration (PP, VC)
10:00–10:30 Coffee break
10:30–11:15 Lecture 10 Introduction to MS based proteomics and Bioconductor infrastructure (LG)
11:15–12:00 Lecture 11 Metagenomics primer (PP)
12:00–14:00 Lunch break (self-organised)
14:00–22:00 Social programme: excursion to the mountains, dinner

Thursday, June 18

08:30–09:15 Lecture 12 Single-cell RNA-Seq (AR, SA)
09:15–10:00 Lecture 13 HiC data analysis (AP)
10:00–10:30 Coffee break
10:30–11:00 Lecture 14 Visualization, the grammar of graphics and ggplot2 (WH)
11:00–11:30 Lecture 03b Multiple testing (WH)
11:30–12:00 Lecture 15 Working with annotation – genes, genomic features and variants (MM)
12:00–14:00 Lunch break (self-organised)
14:00–15:30 Lab 4 Interactive data visualization with Shiny (AO)
15:30–17:00 Lab 5 ChIP-seq analysis basics (AP)
17:00–17:30 Flashlight talks

  • Mariana Ruiz Velasco Leyva
  • Florian Pauler
  • Asaf Peer
  • Antonio Lentini
facultative Lab 6 Graphics (WH)

Friday, June 19

08:30–09:15 Lecture 16 Gene set enrichment analysis (MM, ML)
09:15–10:00 Lecture 17 RNA-Seq data analysis and differential expression part III (ML, SA)
10:00–10:30 Coffee break
10:30–11:15 Lecture 18 Large data, performance, and parallelization; large-scale efficient computation with
genomic intervals (MM, VJC)
11:15–12:00 Lecture 19 Emerging topics
12:00–14:00 Lunch break (self-organised)
14:00–17:00 Lab 7 Machine Learning, Parallelization and performance (WH, MM)
14:00–17:00 Lab 8 Metagenomics (PP)
14:00–17:00 Lab 9 Proteomics (LG)
14:00–17:00 Lab 10 Visualising variants from BAM files (PP)

Flashlight talks

Each talk 5 min + 2 min questions

Lecturers and TAs

Martin Morgan (MM), Vincent J. Carey (VJC), Wolfgang Huber (WH), Simon Anders (SA), Michael Love (ML), Aleksandra Pękowska (AP), Laurent Gatto (LG), Paul Pyl (PP), Alejandro Reyes (AR), Andrzej Oleś (AO), Małgorzata Oleś (MO)