22 Training
The page provides practical information to support training and self-study.
22.1 Checklist
Brief checklist to prepare for training (see below for links).
- Install the recommended software
- If the time allows, watch the short online videos and familiarize yourself with the other available material
- Join Gitter online chat for support
22.2 Recommended software
We recommend installing and setting up the relevant software packages on your own computer as this will support later use. The essential components to install include:
RStudio; choose “Rstudio Desktop” to download the latest version. Check the Rstudio home page for more information. RStudio is optional.
Install key R packages (Section Chapter 1 provides an installation script)
After a successful installation you can consider trying out examples from Section Chapter 24 already before training. You can run the workflows by simply copy-pasting examples. You can then test further examples from this tutorial, modifying and applying these techniques to your own data. Plain source code for the individual chapters of this book are available via Github
If you have access to CSC notebook you can find instructions from here.
22.3 Study material
We encourage you to familiarize yourself with the material and test examples in advance but this is optional:
Introduction to data analysis with R and Bioconductor (for beginners with R)
Short online videos on microbiome data science with R/Bioconductor
Orchestrating Microbiome Analysis with Bioconductor (OMA) (this book)
Chapter 24 for self-study
Chapter 23 and links to complementary external material
22.4 Support and resources
For online support on installation and other matters, join us at Gitter.
You are also welcome to connect through various channels with our broader developer and user community.
22.5 Further reading
The following online books provide good general data science background:
- (Data science basics in R](https://r4ds.had.co.nz)
- (Modern Statistics for Modern Biology)[https://www.huber.embl.de/msmb/] open access book (Holmes S, Huber W)
- The Bioconductor project (background on the Bioconductor project; Carpentries workshop)
22.6 Code of Conduct
We support the Bioconductor Code of Conduct. The community values an open approach to science that promotes:
- sharing of ideas, code, software and expertise
- a kind and welcoming environment, diversity and inclusivity
- community contributions and collaboration