Technical help sheet
During the course some of the practicals make use of a Linux-based command line interface, and R statistical packages. We recommend completing some basic tutorials on this topic in preparation this course. There are many tutorials available online and here are some that may be of help:
- To complete the following suggested tutorials you may want to install Ubuntu for Windows Users if you are using a computer with a Windows Operating System.
- Learn Enough Command Line to Be Dangerous – tutorial
- Learn Enough Command Line to Be Dangerous – manipulating files
- Introduction to R tutorials – Programming basics (if you are completing the R tutorials make sure you complete this one first)
- Introduction to R tutorials – Data Visualization Basics
Regardless of your current knowledge, we encourage everyone to use these, and other materials, to prepare for this course and future work in this area.
Technical requirements for data analysis
You will require following tools for executing the practicals in this course:
Processing zebrafish RNA-seq data using command line and R
- R – https://cran.r-project.org/index.html
- R packages:
- Bioconductor R-package (if identifying differentially expressed genes)
- STAR (if doing the alignment) – https://github.com/alexdobin/STAR
Analysing zebrafish data
- Ensembl – http://www.ensembl.org/index.html
- Cytoscape – https://github.com/cytoscape/cytoscape
- ClueGO – http://www.ici.upmc.fr/cluego/cluegoDocumentation.shtml
- Enrichment Map – https://enrichmentmap.readthedocs.io/en/latest/
- Reactome – https://reactome.org/
- R – https://cran.r-project.org/index.html
- java – https://www.java.com/en/
- Bioconductor R-package (if identifying differentially expressed genes)
- Array Express – https://www.ebi.ac.uk/arrayexpress/
- Expression Atlas – https://www.ebi.ac.uk/gxa/home