4 Getting started

4.1 Checklist

  • Test your login to the CSC R environment (and optionally, set up your own R); see below for details

  • Watch short online videos on microbiome data science with R/Bioconductor.

  • Optionally: Read through the manuscripts in the reading tips (listed below).

  • Try out reproducible reporting Quarto

  • Read about the selected demo data: HintikkaXOData. You can also try to load it in R and explore the data structure.

  • Online support: for installation and other issues, join us at Gitter.

4.2 Study material

The course will use material from OMA online book, which is currently in its beta version. We encourage to familiarize with the content of the book and try some examples already before the course starts but this is optional.

A more extensive checklist for getting started is available, and the slides and other teaching material will be shared at a later point through OMA.

4.2.2 Reading tips

We suggest to read the following manuscripts in order to familiarize with some of the general concepts and approaches discussed at the course.

Software for the Integration of Multiomics Experiments in Bioconductor. Ramos et al. Cancer Res. (2017).

Orchestrating single-cell analysis with Bioconductor. Amezquita, R.A., Lun, A.T.L., Becht, E. et al. Nat Methods 17, 137–145 (2020).

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses. Callahan et al. (2016). F1000Res; 5: 1492.

4.3 Setting up R environment

4.3.1 Your own computer

Setting up your own computer and using local R installation will allow you to continue using the same tools after the course. In order to do this, you can follow the OMA setup checklist.

The course organizers can provide limited online support for installations via Gitter. However, installation is more demanding in some systems.

We also provide the CSC notebook for the course (see below); this comes with all necessary R packages and data pre-installed for ease of use.

4.3.2 CSC Notebook

We provide a temporary access to a cloud computing environment that readily contains the available software packages. Instructions to access the environment will be sent to the registered participants.

  1. Read the instructions
  2. Go to the CSC notebook frontpage
  3. Login
    1. Haka login
      • If you have a Finnish university account, you should be able to login with Haka
      1. Press Login button from the frontpage
      2. Press Haka button
      3. Select right organization
      4. Enter login information
    2. CSC login
      • You can create a CSC account by following the instructions
      1. Press Login button from the frontpage
      2. Press CSC button
      3. Enter login information
    3. Special login
      • For those who cannot login with Haka or CSC account
      1. Contact Giulio on gitter if you are not able to login
      2. We give you a guest account
      3. Press Special Login button from the frontpage (below the Login button)
      4. Enter login information (username goes to email slot)
  4. Join workspace
    1. Press Join workspace button (Top right corner)
    2. Enter the Join Code (Check your email)
  5. Start session
    1. Press ON button
  6. You can save files to my-work directory. They are kept stored even when the session is closed. shared folder is shared with all participants.
Tuomas Borman, and Leo Lahti. 2023. Multi-Omic Data Science with r/Bioconductor. microbiome.github.io.