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JudithBernett merged 7 commits into from
Nov 14, 2025
Merged

restructured data loading, included PDX_Bruna, updated documentation #307

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7d23f92
restructured data loading, included PDX_Bruna, updated documentation
JudithBernett Nov 13, 2025
2852ae8
Merge branch 'development' of github.com:daisybio/drevalpy into devel…
JudithBernett Nov 13, 2025
d24bb62
Merge branch 'development' into pdx_beataml
JudithBernett Nov 13, 2025
995708f
adapt: gene lists are now located in meta
JudithBernett Nov 13, 2025
14096d0
fix: added tissue, comment raytune out for the moment
JudithBernett Nov 13, 2025
47befe3
added pydantic because of https://github.com/ray-project/ray/pull/583…
JudithBernett Nov 14, 2025
edb124f
forfot to add pydantic to the project dependencies
JudithBernett Nov 14, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/run_tests.yml
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Expand Up @@ -13,7 +13,7 @@ jobs:
name: ${{ matrix.session }} ${{ matrix.python-version }} / ${{ matrix.os }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
fail-fast: true
matrix:
include:
- { python-version: "3.13", os: ubuntu-latest, session: "pre-commit" }
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55 changes: 36 additions & 19 deletions docs/usage.rst
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Expand Up @@ -189,24 +189,29 @@ For ``--models``, you can also perform randomization and robustness tests. The `
Available Datasets
------------------
We provide commonly used datasets to evaluate your model on (GDSC1, GDSC2, CCLE, CTRPv2) via the ``--dataset_name`` parameter.

+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------+
| Dataset Name | Number of DRP Curves | Number of Drugs | Number of Cell Lines| Description |
+===================+======================+=================+=====================+==================================================================================================+
| GDSC1 | 316,506 | 378 | 970 | The Genomics of Drug Sensitivity in Cancer (GDSC) dataset version 1. |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------+
| GDSC2 | 234,437 | 287 | 969 | The Genomics of Drug Sensitivity in Cancer (GDSC) dataset version 2. |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------+
| CCLE | 11,670 | 24 | 503 | The Cancer Cell Line Encyclopedia (CCLE) dataset. |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------+
| CTRPv1 | 60,758 | 354 | 243 | The Cancer Therapeutics Response Portal (CTRP) dataset version 1. |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------+
| CTRPv2 | 395,025 | 546 | 886 | The Cancer Therapeutics Response Portal (CTRP) dataset version 2. |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------+
| TOYv1 | 2,711 | 36 | 90 | A toy dataset for testing purposes subsetted from CTRPv2. |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------+
| TOYv2 | 2,784 | 36 | 90 | A second toy dataset for cross study testing purposes. 80 cell lines and 32 drugs overlap TOYv2. |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------+
Further, we provide 2 datasets with more clinical relevance: BeatAML2 and PDX\_Bruna.

+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------------------------+
| Dataset Name | Number of DRP Curves | Number of Drugs | Number of Cell Lines| Description |
+===================+======================+=================+=====================+====================================================================================================================+
| GDSC1 | 316,506 | 378 | 970 | The Genomics of Drug Sensitivity in Cancer (GDSC) dataset version 1. |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------------------------+
| GDSC2 | 234,437 | 287 | 969 | The Genomics of Drug Sensitivity in Cancer (GDSC) dataset version 2. |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------------------------+
| CCLE | 11,670 | 24 | 503 | The Cancer Cell Line Encyclopedia (CCLE) dataset. |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------------------------+
| CTRPv1 | 60,758 | 354 | 243 | The Cancer Therapeutics Response Portal (CTRP) dataset version 1. |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------------------------+
| CTRPv2 | 395,025 | 546 | 886 | The Cancer Therapeutics Response Portal (CTRP) dataset version 2. |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------------------------+
| TOYv1 | 2,711 | 36 | 90 | A toy dataset for testing purposes subsetted from CTRPv2. |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------------------------+
| TOYv2 | 2,784 | 36 | 90 | A second toy dataset for cross study testing purposes. 80 cell lines and 32 drugs overlap TOYv2. |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------------------------+
| BeatAML2 | 62,487 | 166 | 569 (patients) | Ex vivo drug sensitivity screening for a cohort of acute myeloid leukemia (AML) patients. |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------------------------+
| PDX\_Bruna | 2,559 | 104 | 37 (mouse passages) | Ex vivo drug sensitivity screening for short-term cultures of PDTX-derived tumor cells from breast cancer patients |
+-------------------+----------------------+-----------------+---------------------+--------------------------------------------------------------------------------------------------------------------+


If not specifying ``--no_refitting`` option with these datasets (default: false), the desired measure provided with the ``--measure`` option is appended with "_curvecurator", e.g. "IC50_curvecurator".
Expand All @@ -226,16 +231,28 @@ The datasets have corresponding cell-line and drug feature data. The sources are
* CCLE, CTRPv1, CTRPv2:
* Gene expression: reprocessed RNA-seq data PRJNA523380
* Methylation: DepMap Beta Values for RRBS clusters ``CCLE_RRBS_TSS_CpG_clusters_20180614.txt``
* Used by all:
* Used by GDSC1, 2, CCLE, CTRPv1 and v2:
* Mutation & CNV data: `Sanger Cell Model Passports <https://cellmodelpassports.sanger.ac.uk/downloads>`_.
* Proteomics: Raw data at PRIDE: PXD030304
* BeatAML2:
* Gene expression: RNA-seq but not re-processed because of missing FASTQ files. Taken from `the corresponding website <https://biodev.github.io/BeatAML2/>`_
* Mutation data would have been available but is measured too shallow, so we chose not to include it
* PDX\_Bruna:
* Retrieved from `the corresponding figshare <https://figshare.com/s/4a3f6bc543e5ba85834c>`_
* Gene expression: Microarray expression data
* Copy number variation: Reprocessed with GISTIC2.0
* Mutation data would have been available but is measured too shallow, so we chose not to include it
* Methylation data would have been available but only Promoter methylation data which is incompatible with the CpG methylation data we have for the other screens.
* Drug features
* Morgan Fingerprints were generated with RDKit from SMILES either downloaded from PubChem or provided by GDSC.
* `DIPK associated drive <https://drive.google.com/drive/folders/16hP48-noHi3-c_LP9TcZxkwAzqxgR0VB>`_
* MolGNet features were generated from SMILES
* BIONIC features were generated from top expressed genes
* Gene lists
* The 978 landmark genes are from the L1000 assay
* The drug target genes are the genes targeted by the drugs used in GDSC, extractable from the `GDSC Data Portal <https://www.cancerrxgene.org/downloads/bulk_download>`_ (compounds annotation).
* The intersection lists are features occurring in all datasets for the respective OMICs to ensure that cross-study predictions can easily be done because the features are shared.
* Reduced versions of the lists only containing genes occurring in all datasets

For more information on the preprocessing, please refer to `the corresponding GitHub Repo <https://github.com/daisybio/preprocess_drp_data>`_.

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