The generation of the real datasets is divided in two parts. We first download all the (annotated) expression files from sites such as GEO. Next, we filter and normalise all datasets, and wrap them into the common trajectory format of dynwrap.
| # | script/folder | description |
|---|---|---|
| 1 | 📄download_from_sources.R |
Downloading the real datasets from their sources (eg. GEO), and constructing the gold standard model, using the helpers in helpers-download_from_sources |
| 2 | 📄filter_and_normalise.R |
Filtering and normalising the real datasets using dynbenchmark::process_raw_dataset All datasets are then saved into the dynwrap format. |
| 3 | 📄gather_metadata.R |
Gathers some metadata about all the real datasets |
| 4 | 📄datasets_table.R |
Creates a table of the datasets in, excuse me, excel (for supplementary material) |
📁helpers-download_from_sources |