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doc: improve readme
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BorisMuzellec authored Dec 5, 2024
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# Datasets organisation
# FedPyDESeq2 datasets

This directory contains the data, assets and scripts necessary to:
This repository complements [FedPyDESeq2](https://github.com/owkin/fedpydeseq2), by providing scripts to download and preprocess the
[TCGA](https://www.cancer.gov/tcga) data used in the FedPyDESeq2 preprint.

More precisely, it contains the data, assets and scripts necessary to:
- download the raw data necessary to run the tests and experiments, when not
available in the repository, in the `download_data` directory;
- open the data when performing a Substra experiment in the `assets` directory;
- store the data in the `data` directory.

## Installation

You can install the package from PyPI using the following command:

`pip install fedpydeseq2-datasets`

## Data download

For a detailed description of the data download process, please refer to the
Expand All @@ -14,7 +23,6 @@ For a detailed description of the data download process, please refer to the
If you want to run the pipeline directly, you can use the script which is available in the distribution: `fedpydeseq2-download-data`



```bash
fedpydeseq2-download-data
```
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