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Perturbation-Response-Prediction / PRnet

PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.
Apache License 2.0
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lack of dataset file #3

Closed younng367 closed 2 days ago

younng367 commented 1 month ago

could you upload the dataset file?Please~ Dear professor

nicole1q commented 1 month ago

If the links fail to redirect, please download the corresponding data and pretrained model weights from: http://prnet.drai.cn/Statistics/. For the data files, download LINCS L1000 Chemical Perturbations and Sci-plex Chemical Perturbations from the Supplementary Dataset section. For the model weights, download the PRnet model from the Supplementary Dataset section.

Jianbo1999 commented 1 month ago

Hello, where is the data: FDA_drug_fold-change_2W.csv

nicole1q commented 1 month ago

If the links fail to redirect, please download the corresponding data and pretrained model weights from: http://prnet.drai.cn/Statistics/. For the data files, download LINCS L1000 Chemical Perturbations and Sci-plex Chemical Perturbations from the Supplementary Dataset section. For the model weights, download the PRnet model from the Supplementary Dataset section. Then change the names of the datasets to Lincs_L1000.h5ad and Sci_Plex.h5ad respectively. If the dataset cannot be downloaded, please adjust your browser settings to allow insecure content on the current webpage by setting it to "Allow."

Jianbo1999 commented 1 month ago

I would like to find a similar molecule to my small molecule (I had transcriptomics data) using the PRnet. How can I do it?

nicole1q commented 1 month ago

Hello, where is the data: FDA_drug_fold-change_2W.csv

Please download the corresponding data from: http://prnet.drai.cn/Statistics/. ‘FDA_drug_fold-change_2W.csv’: download the FDA-approved Drugs Signatures from the PRnet Predicted Transcriptional Signatures section.

nicole1q commented 1 month ago

I would like to find a similar molecule to my small molecule (I had transcriptomics data) using the PRnet. How can I do it?

I don't quite understand, could you describe it in more detail?

Jianbo1999 commented 1 month ago

I would like to find a similar molecule to my small molecule (I had transcriptomics data) using the PRnet. How can I do it?

I don't quite understand, could you describe it in more detail?

I have transcriptome and structural data of a small molecule, and I want to find similar molecules for target screening using the PRnet method

nicole1q commented 3 weeks ago

I would like to find a similar molecule to my small molecule (I had transcriptomics data) using the PRnet. How can I do it?

I don't quite understand, could you describe it in more detail?

I have transcriptome and structural data of a small molecule, and I want to find similar molecules for target screening using the PRnet method

To prepare your dataset for a new small molecule, please refer to the instructions in custom_data_preprocessing.ipynb. Once your dataset is ready, you can predict the perturbed expression profile by running test_demo.py, adjusting the split_key argument as needed for your analysis.

If you’re interested in other applications or discussing potential collaborations, please feel free to reach out at biozy@ict.ac.cn.