Programme

Sunday, July 21

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

Monday, July 22

08:30–09:15 Lecture 01 Introduction to R and Bioconductor (MM)
09:15–10:00 Lecture 02 Linear models (basic intro) (RG)
10:00–10:30 Coffee break
10:30–11:15 Lecture 03 Using Bioconductor for computing with sequences and ranges (LS)
11:15–12:00 Lecture 04 Hypothesis testing incl. multiple (WH)
12:00–13:00 Lunch break
13:00–13:30   Installation help desk
13:30–15:00 Lab 1 Introduction to Bioconductor (MM)
15:00–16:30 Lab 2 Multiple testing, FDR (WH)
16:30–17:00 Flashlight talks
  • Monika Pepelnjak
  • Maximilian J. Helf
  • Petra Svatonova
  • Domenico di Fraia
20:10–22:00 Evening session  
20:10–20:30   Beer and pizza will be provided
20:30–21:15  
  • Session 1: Bioconductor in containers (Nitesh Turaga)
  • Session 2: Reproducible research with Rmarkdown, git and github (LG)
21:15–22:00 Discussion sessions
  • Experimental design questions and answers
  • Implementing open and reproducible research in my day to day work
  • Hyperlinked reports and apps instead of printouts / CSVs — Globally accessible analyses and data via shinyapps.io
  • … (please add your suggestion via the slack channel) …

Tuesday, July 23

08:30–09:15 Lecture 05 Quantification (both alignment and alignment-free) (CS)
09:15–10:00 Lecture 06 Normalization and differential expression (SA)
10:00–10:30 Coffee break
10:30–11:00 Lecture 07 Single-cell technology (incl. Announcement of group project) (KI, DR)
11:00–12:00 Lecture 08 Annotation resources. (LS with JR)
12:00–13:30 Lunch break
13:30–16:30 Lab 3 End-to-end RNA-Seq workflow (SA, CS, DR, WH, JR)
16:30–17:00 Flashlight talks
  • Staci Thornton
  • Fabienne Meier-Abt
  • Inigo Barrio
  • Henry F. Thomas
20:10–22:00 Evening session  
20:10–20:30   Beer and pizza will be provided
20:30–21:15  
  • Creating and maintaining an R package (DR), Aula B
  • Interactive visualization (SA) + 5 min iSEE demo (CS), Aula Magna
21:15–22:00  
  • ChIP-Seq, ATAC-Seq (DR, WH, VJC, KI), Garden chairs discussion
  • Effective R code, debugging, timing (MM), Aula Magna

Wednesday, July 24

08:30–09:15 Lecture 09 Experimental design, batch effects and ‘correction’, confounding (CS)
09:15–10:00 Lecture 10 eQTLs, sQTLs (RG)
10:00–10:30 Coffee break
10:30–11:15 Lecture 11 Single-cell data analysis I: error models, normalization, factor analysis, (ZI)NB-WaVE (DR)
11:15–12:00 Lecture 12 Single-cell data analysis II: factor analysis, dimension reduction (“t-SNE”), cell type assignment (SA)
12:00–13:30 Lunch break
14:00–22:30   Social programme: excursion to the mountains, dinner

Thursday, July 25

08:30–09:15 Lecture 13 Visualization, grammar of graphics and ggplot2 (WH)
09:15–10:00 Lecture 14 Mass spec proteomics (LG)
10:00–10:30 Coffee break
10:30–11:00 Lecture 15 Metabolomics (JR)
11:00–11:45 Lecture 16 Clustering and classification (VJC)
11:45–12:00   BiocFileCache / Annotation resources (LS)
12:00–13:30 Lunch break
13:30–16:30 Lab 4 Mass spec proteomics (LG)
13:30–16:30 Lab 5 Preprocessing of untargeted metabolomics data (JR)
13:30–16:30 Lab 6 BiocFileCache / Annotation resources (LS)
13:30–16:30   Group work on single cell technologies (KI)
16:30–17:00 Flashlight talks
  • Amir Fallahshahroudi
  • Constantin Ahlmann-Eltze
  • Thomas Naake

Friday, July 26

08:30–09:15 Lecture 17 High-throughput genetics – CRISPR screens analysis (KI)
09:15–10:00 Lecture 18 Machine Learning (RG)
10:00–10:30 Coffee break
10:30–11:15 Lecture 19 Gene set enrichment analysis (MM)
11:15–12:00 Lecture 20 Working with large-scale data (MM with VJC)
12:00–13:30 Lunch break
13:30–14:00   Presentations from group work on single-cell technologies
14:00–16:30 Lab 7 Single-cell sequencing analysis workflow (SA, DR)
14:00–16:30 Lab 8 Interactive visualisation of SummarizedExperiments: iSEE (CS)
14:00–16:30 Lab 9 Large data, performance, and parallelization (VJC, MM)
14:00–16:30 Lab 10 Machine learning (supervised) (WH)
16:30   Closing remarks

Flashlight talks

Each talk 5 min + 2 min questions

Lecturers and Teaching Assistants

Simon Anders (SA), Simone Bell (SB), Vincent J. Carey (VJC), Laurent Gatto (LG), Robert Gentleman (RG), Wolfgang Huber (WH), Katharina Imkeller (KI), Martin Morgan (MM), Davide Risso (DR), Mike Smith (MS), Johannes Rainer (JR), Lori Shepherd (LS), Charlotte Soneson (CS).