Hello CRISPRon team,
Thank you for making the CRISPRon code and pretrained models publicly available. I am currently trying to reproduce the DeepCRISPRon model described in your paper:
Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning (Nature Communications, 2021).
I have downloaded the GitHub repository and the provided Luo2020_Kim2019 dataset. However, I noticed that the training script (DeepCRISPRon_train.py) requires input files such as:
validation_set1.csv
validation_set2.csv
...
validation_set6.csv
with columns including:
30mer_gRNA
Quant_norm_efficiency
CRISPRoff
I could not find these processed training files in the GitHub repository or the downloaded dataset package.
Could you please let me know whether these training partition files are publicly available somewhere, or if there is a recommended preprocessing pipeline to generate them from the provided datasets?
I would also appreciate any guidance regarding how the Quant_norm_efficiency values and the CRISPRoff feature were generated for the released training data.
Thank you very much for your help and for sharing this valuable resource.
Best regards,
Lin
Hello CRISPRon team,
Thank you for making the CRISPRon code and pretrained models publicly available. I am currently trying to reproduce the DeepCRISPRon model described in your paper:
Enhancing CRISPR-Cas9 gRNA efficiency prediction by data integration and deep learning (Nature Communications, 2021).
I have downloaded the GitHub repository and the provided Luo2020_Kim2019 dataset. However, I noticed that the training script (DeepCRISPRon_train.py) requires input files such as:
with columns including:
I could not find these processed training files in the GitHub repository or the downloaded dataset package.
Could you please let me know whether these training partition files are publicly available somewhere, or if there is a recommended preprocessing pipeline to generate them from the provided datasets?
I would also appreciate any guidance regarding how the Quant_norm_efficiency values and the CRISPRoff feature were generated for the released training data.
Thank you very much for your help and for sharing this valuable resource.
Best regards,
Lin