Bioinformatics & Functional Genomics in Zebrafish 2019

This page has links to materials and example data used during the Bioinformatics & Functional Genomics in Zebrafish course run in 2019 at the European Bioinformatics Institute.

Guidelines for Experimental Design

• Slides (1.5 MB PDF)

Day 1: Command Line for Data Filtering

• Slides (2.9 MB PDF)
• Exercises (60 KB PDF) + Answers (85 KB PDF)
• example.tsv (3.6 MB TSV)
• myc-targets.tsv (1.1 KB TSV)

Day 1: Data Visualisation with R

• Slides (6.4 MB PDF)
• Exercises (56 KB PDF) + Answers
• example2.tsv (37 MB TSV)

Day 3: Zebrafish Anatomical Term Enrichment

• Slides (422 KB PDF)
• zfa.obo (1.3 MB)
• ensembl.ids (2 MB)
• population.tsv (604 KB TSV)
• study.tsv (46 KB TSV)

Day 3: Cytoscape for Visualisation

• Slides (6.1 MB PDF)
• uninf_3dpf_hom_vs_uninf_3dpf_sib.nodes.tsv (17 KB TSV)
• uninf_3dpf_hom_vs_uninf_3dpf_sib.edges.tsv (79 KB TSV)
• uninf_3dpf_hom_vs_uninf_3dpf_sib.sif (57 KB)
• cluego-notes.txt
• correlation-network-from-expr.R

Zebrafish Dataset

• Description (115 KB PDF)
• Day 1: Practical 1 (126 KB PDF) + Answers
• Day 2: Practical 2 (47 KB PDF) + Answers (94 KB PDF)
• Day 3: Practical 3 (61 KB PDF)
• Day 4: Practical 4 (62 KB PDF)
• deseq2-results.tsv (57 MB TSV)
• samples.tsv (3.2 KB TSV)