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JaneJiayiDong / GROD

The official implementation of "GRODE: Joint Inference of Gene Regulatory Networks and Data Imputation in Single-Cell RNA Sequencing with Temporal Consideration".
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dataset request #1

Closed prsigma closed 6 months ago

prsigma commented 6 months ago

Hi, thanks for your awesome work, could you please provide the datasets for training?

JaneJiayiDong commented 6 months ago

The dataset for gene regulatory network inference uses Beeline. Sorry, I will add relevant documentation soon.

prsigma commented 6 months ago

The dataset for gene regulatory network inference uses Beeline. Sorry, I will add relevant documentation soon.

Hello, I'm glad to see your prompt response, but I noticed that the 'expression.csv' file you uploaded is empty. Also, could you please upload the 'tfs+500' and 'tfs+1000' datasets used in the paper? It seems that the 'Beeline' paper did not release these datasets. thanks！

JaneJiayiDong commented 6 months ago

Sorry, I reupload the data (mESC_tfs+500) and the complete dataset needs some time to be sorted and uploaded. And you can try to use code(generateExpInputs.py) in Beeline and raw data in https://zenodo.org/records/3701939 to generate these related datasets.

prsigma commented 6 months ago

Sorry, I reupload the data (mESC_tfs+500) and the complete dataset needs some time to be sorted and uploaded. And you can try to use code(generateExpInputs.py) in Beeline and raw data in https://zenodo.org/records/3701939 to generate these related datasets.

Thank you for your response. I have reviewed the generateExpInputs.py code in BEELINE, and it does indeed generate the tfs+500 and tfs+1000 datasets. However, it requires human and mouse transcription factor (TF) databases file, and it seems these files are not included at https://zenodo.org/records/3701939. Where can I obtain these TF databases files? thanks very much!

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JaneJiayiDong commented 6 months ago

You can download this file in https://zenodo.org/records/3701939. image image

prsigma commented 6 months ago

You can download this file in https://zenodo.org/records/3701939. image image

Got it! Thank you for your enthusiastic, prompt, and detailed response. wish you happiness every day.