Metadata-Version: 2.1
Name: spectrum-utils
Version: 0.4.1
Summary: Mass spectrometry utility functions
Home-page: https://github.com/bittremieux/spectrum_utils
Author: Wout Bittremieux
Author-email: wbittremieux@health.ucsd.edu
License: Apache 2.0
Project-URL: Documentation, https://spectrum-utils.readthedocs.io/
Project-URL: Bug Tracker, https://github.com/bittremieux/spectrum_utils/issues
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: MacOS
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: appdirs
Requires-Dist: fastobo
Requires-Dist: lark (>=1.0)
Requires-Dist: matplotlib
Requires-Dist: numba (>=0.47)
Requires-Dist: numpy
Requires-Dist: pyteomics (>=4.5)
Provides-Extra: dev
Requires-Dist: black ; extra == 'dev'
Requires-Dist: pytest ; extra == 'dev'
Requires-Dist: pytest-cov ; extra == 'dev'
Provides-Extra: docs
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Requires-Dist: numpydoc (>=1.1.0) ; extra == 'docs'
Requires-Dist: sphinx (>=3.5.3) ; extra == 'docs'
Requires-Dist: sphinx-rtd-theme (>=0.5.1) ; extra == 'docs'
Requires-Dist: sphinx-markdown-tables ; extra == 'docs'
Provides-Extra: iplot
Requires-Dist: altair ; extra == 'iplot'
Requires-Dist: pandas ; extra == 'iplot'

# spectrum_utils

[![conda](https://img.shields.io/conda/vn/bioconda/spectrum_utils?color=green)](http://bioconda.github.io/recipes/spectrum_utils/README.html)
[![PyPI](https://img.shields.io/pypi/v/spectrum_utils?color=green)](https://pypi.org/project/spectrum_utils/)
[![Build status](https://github.com/bittremieux/spectrum_utils/workflows/tests/badge.svg)](https://github.com/bittremieux/spectrum_utils/actions?query=workflow:tests)
[![docs](https://readthedocs.org/projects/spectrum_utils/badge/?version=latest)](https://spectrum_utils.readthedocs.io/en/latest/?badge=latest)

spectrum_utils is a Python package for efficient mass spectrometry data processing and visualization.

spectrum_utils contains the following features:

- Spectrum loading from online proteomics and metabolomics data resources using the [Universal Spectrum Identifier (USI)](https://www.psidev.info/usi) mechanism.
- Common spectrum processing operations (precursor & noise peak removal, intensity filtering, intensity scaling) optimized for computational efficiency.
- Annotating observed spectrum fragments using the [ProForma 2.0 specification](https://www.psidev.info/proforma) for (modified) peptidoforms.
- Publication-quality, fully customizable spectrum plotting and interactive spectrum plotting.

## Installation

spectrum_utils requires Python version 3.8+ and can be installed with pip or conda.

Using pip:

    pip install spectrum_utils[iplot]

Using conda:

    conda install -c bioconda spectrum_utils

## Documentation

Please see the [documentation](https://spectrum-utils.readthedocs.io/) for detailed installation instructions, usage examples, the API reference, and more information.

## Citation
 
spectrum_utils is freely available as open source under the [Apache 2.0 license](http://opensource.org/licenses/Apache-2.0).

When using spectrum_utils, please cite the following manuscripts:
 
- Wout Bittremieux. "spectrum_utils: A Python package for mass spectrometry data processing and visualization." _Analytical Chemistry_ **92**, 659--661 (2020) doi:[10.1021/acs.analchem.9b04884](https://doi.org/10.1021/acs.analchem.9b04884).
- Wout Bittremieux, Lev Levitsky, Matteo Pilz, Timo Sachsenberg, Florian Huber, Mingxun Wang, Pieter C. Dorrestein. "Unified and standardized mass spectrometry data processing in Python using spectrum_utils" _bioRxiv_ (2022).
