- recipe mhcnuggets
MHCnuggets: Neoantigen peptide MHC binding prediction for class I and II
- Homepage:
- License:
APACHE / Apache License
- Recipe:
# MHCnuggets
Welcome to MHCnuggets! Presumably you're here to do some peptide-MHC prediction and not because you were [hungry](https://www.mcdonalds.com/us/en-us/product/chicken-mcnuggets-4-piece.html).
### Usage ### For an overview of how to use MHCnuggets please refer to the Jupyter notebook called `user_guide.ipynb` in the repository
### Installation ###
MHCnuggets is `pip` installable as: ```bash pip install mhcnuggets ```
**Required pacakges:**
* numpy * scipy * scikit-learn * tensorflow * keras
You might want to check if the Keras backend is configured to use the Tensforflow backend.
- package mhcnuggets¶
- Versions:
2.4.1-0,2.4.0-0,2.3.2-0,2.3.1-0,2.2-0- Depends:
on keras
on numpy
on pandas
on python
3.6.*on scikit-learn
on scipy
on tensorflow
on varcode
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install mhcnuggets
to add into an existing workspace instead, run:
pixi add mhcnuggets
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install mhcnuggets
Alternatively, to install into a new environment, run:
conda create -n envname mhcnuggets
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/mhcnuggets:<tag>
(see mhcnuggets/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/mhcnuggets/README.html)
