This repository contains the materials for the course "Bioinformatic approaches to regulatory genomics and epigenomics" (ETH 376-1347-00L)
You can create your own copy of the repository using the Fork button (top right).
For questions/communication, use the slack workspace.
| W | Date | Lecture (~30min) | Mixed/hands-on (~60min) |
|---|---|---|---|
| 1 | 02.20 | Introduction to the course | Introduction to the practical tools for the course |
| 2 | 02.27 | Genome builds, transcriptome assemblies and annotations | AnnotationHub, Genomic Ranges, Features and their manipulating in R |
| 3 | 03.06* | Overview of NGS chromatin assays and their analysis | Primary ChIPseq analysis pipeline |
| 4 | 03.13 | QC, functional elements & the histone code | Finding data, data visualization and exploration |
| 5 | 03.20 | Differential analysis and normalization | Differential analysis and normalization |
| 6 | 03.27 | Types of transcriptional regulators, modes and dynamics of their binding | Motif analysis |
| * | 04.03 | ###### Spring break - No Course ###### | |
| * | 04.10 | ###### Spring break - No Course ###### | |
| 7 | 04.17 | DNA accessibility, nucleosome positioning, and TF footprints | Analysis and exploration of ATAC-seq data |
| 8 | 04.24 | DNA methylation and CpG islands | DNAme analysis and visualization |
| * | 05.01 | ###### Labour day - No Course | |
| 9 | 05.08 | From repression to expression and back | Clustering genomic signals and characterizing the clusters |
| 10 | 05.15# | Chromatin conformation, domains and looping | Working with distal regulatory elements |
| 11 | 05.22 | Multi-modal integration | Multi-modal integration |
| 12 | 05.29 | Single-cell chromatin assays; chromatin and disease; open questions |
Projects |
- \* I'm away on the 6th of March, and the course will be held online.
- # On the 15th of may there is teaching, but since the 14th is a holiday and many people are away, there will be the option to join online and the class will be recorded.
As I am making adjustments to the course this year, the course plan is subject to change.