mhcnuggets

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Predict import fails after installation using pip

5

After installing MHCnuggets using `pip` (`pip install mhcnuggets`), the import `from mhcnuggets.src.predict import predict` fails. ``` python Python 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 05:59:23) [Clang...

christopher-mohr

Request supplementary methods for HLA class II immunogenic mutation burden predicts response to immune checkpoint blockade

4

Hi, I just downloaded the manuscript for HLA class II immunogenic mutation burden predicts response to immune checkpoint blockade, and trying to get more details regarding the methods. Can you...

xiw588

Tensorflow version

1

Hello, current releases of both https://github.com/griffithlab/pVACtools and https://github.com/openvax/mhcflurry doesn't support tensorflow 2.0.0+ and have limitation for tensorflow version: `tensorflow>=1.15.0,

Stikus

mhcnuggets scores on TESLA samples

4

I was very curious to test the performance of mhcnuggets 2.3 on the latest dataset with TESLA validated neoantigen candidates published in Cell ([Key Parameters of Tumor Epitope Immunogenicity Revealed...

vladimirkovacevic

Feature request: allow for silent/verbose mode

3

Dear MHCnuggets maintainer, I have written [a package](https://github.com/richelbilderbeek/mhcnuggetsr) to call MHCnuggets from R. However, when I call the `predict` function, MHCnuggets produces output, which (1) I cannot prevent, and (2)...

richelbilderbeek

Feature request: add continuous integration

8

Dear MHCnuggets maintainer, MHCnuggets appears awesome to me! But without any form of continuous integration, one cannot verify if indeed everything (still) works. Also, a CI install script shows all...

richelbilderbeek

Input format

1

Hi Rohit, I was trying to use the 'predict' method from mhcnuggets. Currently based on the user_guide notebook one can only provide the peptide sequence as a file. Is there...

amomin-pact

Feature request: use Python3

1

From [here](https://github.com/KarchinLab/mhcnuggets/issues/11#issuecomment-633513108) I quote @XiaoshanShao: > We built MHCnuggets mostly on python2 instead of python3. Although we built it to be indifferent to python versions, it could be one aspect...

richelbilderbeek

Although MHCnuggets appears awesome, there are no tests to prove that it works correctly. I would enjoy be able to be sure that MHCnuggets at least works on some minimal...

richelbilderbeek

Hello, as you can see in pVACtools issue https://github.com/griffithlab/pVACtools/issues/1084 - https://github.com/openvax/mhcflurry and mhcnuggets doesn't work with latest [2.16.1 version of tensorflow](https://github.com/tensorflow/tensorflow/releases/tag/v2.16.1). ``` Exception: An error occurred while calling MHCnuggets: /usr/local/lib/python3.10/dist-packages/keras/src/layers/core/masking.py:47:...

Stikus