- recipe peptdeep
The AlphaX deep learning framework for Proteomics
- Homepage:
- Documentation:
- License:
APACHE / Apache-2.0
- Recipe:
PeptDeep provides deep learning models for mass spectrometry-based proteomics. It includes built-in models for predicting retention time, collision cross section, and tandem mass spectra for peptides, enabling users to generate predicted spectral libraries from protein sequences.
- package peptdeep¶
- versions:
1.4.1-1,1.4.1-0- depends alphabase:
>=1.5.0- depends alpharaw:
>=0.2.0- depends click:
- depends lxml:
- depends numba:
- depends numpy:
<2- depends pandas:
<3.0- depends psutil:
- depends pyteomics:
- depends python:
>=3.8- depends pytorch:
- depends scikit-learn:
- depends tqdm:
- depends transformers:
- requirements:
- additional platforms:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install peptdeep and update with:: mamba update peptdeep
To create a new environment, run:
mamba create --name myenvname peptdeep
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/peptdeep:<tag> (see `peptdeep/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/peptdeep/README.html)
