Bioinformatics & Functional Genomics in Zebrafish 2022
This page has links to materials and example data used during the Bioinformatics & Functional Genomics in Zebrafish course run in 2022 at the European Bioinformatics Institute.
Day 1: Guidelines for Experimental Design
- Slides (1.5 MB PDF)
Day 1: Group Metadata Exercise
- Slides (82 KB PDF)
Day 1: Command Line for Data Filtering
- Slides (3.3 MB PDF)
- Exercises (154 KB PDF) + Answers
- Oxy.counts.tsv (12 MB TSV)
- brain-development.txt (6 KB)
Day 1: Data Visualisation with R
Day 2: Ensembl
Day 2: Extra Ensembl
- Slides (2.6 MB PDF)
Day 3: Gene Ontology
- Slides (6.9 MB PDF)
Day 3: Reactome
Day 3: Cytoscape
- Slides (4.5 MB PDF)
- Amp.edges.txt (743 KB)
- Amp.nodes.txt (25 KB)
- Amp.sif (524 KB)
- Amp.topgo.gmt (307 KB)
- Oxy.topgo.gmt (433 KB)
- Amp.BP.topgo.sig.tsv (7 KB)
- Oxy.BP.topgo.sig.tsv (6 KB)
- Amp.de.network.R (2 KB)
- enrichment-map-files.pdf (257 KB PDF)
Day 3: ZFA Enrichment
- Slides (532 KB PDF)
- zfin.txt (17 MB)
- zfa.obo (1.5 MB)
- Ontologizer.jar (678 KB)
Day 3: Extra BioMart
- biomaRt tutorial (74 KB PDF)
Day 4: Expression Atlas
- Slides 1
- Slides 2
- Slides 3
- Exercise - Single Cell Expression Atlas
- Exercise - Expression Atlas - Differential Expression
- Exercise - Expression Atlas - Baseline Expression
- Exercise - ArrayExpress
Zebrafish Dataset
- Description (243 KB PDF)
- Day 1: Practical 1 (5.6 MB PDF) + Solutions
- Day 2: Practical 2 (64 KB PDF) + Solutions
- Day 3: Practical 3 (117 KB PDF)
- Day 4: Practical 4 (118 KB PDF)
- Amp.counts.tsv (12 MB TSV)
- Amp.samples.tsv (<1 KB TSV)
- Oxy.counts.tsv (12 MB TSV)
- Oxy.samples.tsv (<1 KB TSV)
- Nic.counts.tsv (11 MB TSV)
- Nic.samples.tsv (<1 KB TSV)