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:
docker/- all container information necessary for running notebookssession_preparation/- data pre-processing, feature selection and dimensionality reductionsession_ml/- the machine learning sessions, days 1 and 2session_topology/- the network topology analysis, day 3 morningsession_meta/- network meta-analysis, day 3 afternoonenvironments/- legacy conda environments
You will need to create the two docker containers to run with each of the notebooks.
Environments
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 |