Chenkai Li

Results 6 comments of Chenkai Li

Package excluded by strict repo priority

Finally passed the tests by loosening the tensorflow version constraint to be >=1.10,

AMP seq identified as non-amp

Hi @Darcy220606, Thanks for contacting us for your issue. Yes, the model was trained with mature sequences and part of them are from APD3. Were the sequences in your test...

AMP seq identified as non-amp

Hi @Darcy220606 Since the negative samples we used for training the model is very different from other tools (we applied more stringent criteria to select non-AMP sequences), so it is...

Blas xGEMMBatched launch failed

Hi @narib, Which tensorflow and keras versions are you using? Cheers, Chenkai

How to use GPU for prediction

To run AMPlify on GPU, you need to install tensorflow-gpu (1.12.0) instead of the default tensorflow. You may also add some codes like these to the beginning of your script:...

Input Sequences

Hi @Kudzai-H, Thanks for contacting us regarding your questions. Yes, the AMPlify inputs have to be protein sequences. We have developed an AMP discovery pipeline ([https://github.com/bcgsc/rAMPage](https://github.com/bcgsc/rAMPage)) which takes RNA-seq reads...