Metadata-Version: 2.1
Name: spectrum-utils
Version: 0.3.5
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
Platform: UNKNOWN
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: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: matplotlib
Requires-Dist: numba (>=0.47)
Requires-Dist: numpy
Requires-Dist: pyteomics
Provides-Extra: dev
Requires-Dist: flake8 ; extra == 'dev'
Provides-Extra: docs
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: recommonmark (>=0.7.1) ; 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 MS/MS spectrum processing and
visualization.

spectrum_utils contains the following features:

- Spectrum processing
    - Precursor & noise peak removal
    - Intensity filtering
    - Intensity scaling
    - Peak annotations
        - Modification-aware (static & variable) peptide fragments
        - SMILES-based molecules
        - Custom strings
- Spectrum plotting
    - Fully customizable individual spectrum plots
    - Mirror plot of matching spectra
    - Interactive spectrum plots

![spectrum_utils](spectrum_utils.png)

## Installation

spectrum_utils requires Python version 3.6+ and can be installed with pip or
conda.

Using conda:

    conda install -c bioconda spectrum_utils

Using pip:

    pip install 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 manuscript:

Wout Bittremieux. "spectrum_utils: A Python package for mass spectrometry data
processing and visualization." _Analytical Chemistry_ 92 (1) 659-661 (2020)
doi:[10.1021/acs.analchem.9b04884](https://doi.org/10.1021/acs.analchem.9b04884).


