ethepigen2024_materials's Introduction

Regulatory genomics - Materials 2024

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.

Provisional course plan

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

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