ethepigen2023_materials's Introduction

Regulatory genomics - Materials 2023

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	24/02	Introduction to the course	Introduction to the practical tools for the course
2	03/03	Genome builds, transcriptome assemblies and annotations	AnnotationHub, Genomic Ranges, Features and their manipulating in R
3	10/03	Overview of NGS chromatin assays and their analysis	Primary ChIPseq analysis pipeline
4	17/03	Specificities and QCs on primary analysis	Finding data from the literature
5	24/03	Functional elements & the histone code	Visualization and exploration of histone modifications
6	31/03	Types of transcriptional regulators, modes and dynamics of their binding	Motif analysis
*	07/04	###### Easter - No Course ######
*	14/04	###### Easter - No Course ######
7	21/04	DNA accessibility, nucleosome positioning, and TF footprints	Analysis and exploration of ATAC-seq data
8	28/04	Differential analysis	Differential analysis
9	05/05	Normalization and enrichment analysis	Normalization and enrichment analysis
10	12/05	From repression to expression and back	Clustering genomic signals and characterizing the clusters
11	19/05	DNA methylation and CpG islands	DNAme visualization
12	26/05	Chromatin conformation, domains and looping	Working with distal regulatory elements
13	02/05	Single-cell chromatin assays; chromatin and disease; open questions

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