This repository contains the materials for the course "Bioinformatic approaches to regulatory genomics and epigenomics" (ETH 376-1347-00L)
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| W | Date | Lecture (~30min) | Mixed/hands-on (~60min) |
|---|---|---|---|
| 1 | 23/02 | Introduction to the course | Introduction to the practical tools for the course |
| 2 | 01/03 | Genome builds, transcriptome assemblies and annotations | AnnotationHub, Genomic Ranges, Features and their manipulating in R |
| 3 | 08/03 | Overview of NGS chromatin assays and their analysis | Primary ChIPseq analysis pipeline |
| 4 | 15/03 | Specificities and QCs on primary analysis | Finding data from the literature |
| 5 | 22/03 | Functional elements & the histone code | Visualization and exploration of histone modifications |
| * | 29/03 | ###### Easter - No Course ###### | |
| * | 05/04 | ###### Easter - No Course ###### | |
| 6 | 12/04 | Types of transcriptional regulators, modes and dynamics of their binding | Motif analysis |
| 7 | 19/04 | DNA accessibility, nucleosome positioning, and TF footprints | Analysis and exploration of ATAC-seq data |
| 8 | 26/04 | Differential analysis | Differential analysis |
| 9 | 03/05 | Normalization and enrichment analysis | Normalization and enrichment analysis |
| 10 | 10/05 | From repression to expression and back | Clustering genomic signals and characterizing the clusters |
| 11 | 17/05 | DNA methylation and CpG islands | DNAme visualization |
| 12 | 24/05 | Chromatin conformation, domains and looping | Working with distal regulatory elements |
| 13 | 31/05 | Single-cell chromatin assays; chromatin and disease; open questions |