Lab instructions

Clone the course repository

Ensure that you have followed all the installation instructions. In each container you will find a folder workshop/ that contains the latest version of the repository. Inside you find:

You will need to create the two docker containers to run with each of the notebooks.


See the pre-course installation to setup and start the docker containers. For notebooks that are in Rmd you should use the rstudio container, whereas for the ipynb notebooks you should use the jupyter container. If you cannot setup and run these notebooks, each directory also contains the respective HTML files to assist you.
Please refer to the next list of notebooks and environments:

Topic notebook type path to notebook HTML file container
Data pre-processing ipynb /session_preparation/data_preparation/preprocessing.ipynb html jupyter
Dimensionality reduction Rmd /session_preparation/dimreduction/OmicsIntegration_DimensionReduction.Rmd html rstudio
Feature selection Rmd /session_preparation/feature_selection/OmicsIntegration_FeatureSelection.Rmd html rstudio
Supervised Integration Rmd /session_ml/SupervisedOMICsIntegration/supervised_omics_integr_CLL.Rmd html rstudio
Unsupervised Integration Rmd /session_ml/UnsupervisedOMICsIntegration/UnsupervisedOMICsIntegration.Rmd html rstudio
Network analysis ipynb /session_topology/lab.ipynb html jupyter
Network meta analysis Rmd /session_meta/lab_meta-analayses-v2.Rmd html to create from within R