Add notebooks to align genes in sciplex and lincs datasets

theislab / chemCPA

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

https://arxiv.org/abs/2204.13545

MIT License

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Add notebooks to align genes in sciplex and lincs datasets #50

Closed MxMstrmn closed 2 years ago

MxMstrmn commented 2 years ago

Requirements are mentioned in the respective notebooks. First run the gene_matching notebook. Subsequently, add smiles strings. Added the PROJECT_DIR to the paths file. Resulting h5ad files are stored in 'PROJECT_DIR/datasets/'.

Related to #34

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siboehm commented 2 years ago

To be fixed:

The smiles for the control drug is CS(C)=O, however in the new datasets it's just empty (null).
In the new Trapnell dataset there is a drug called (+)-JQ1 which is just called JQ1 in the old dataset.