pyteomics

A framework for proteomics data analysis.

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Project links

Homepage

Project description

What is Pyteomics?

Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common tasks in proteomics data analysis, such as:

calculation of basic physico-chemical properties of polypeptides:
- mass and isotopic distribution
- charge and pI
- chromatographic retention time
access to common proteomics data:
- MS or LC-MS data
- FASTA databases
- search engines output
easy manipulation of sequences of modified peptides and proteins

The goal of the Pyteomics project is to provide a versatile, reliable and well-documented set of open tools for the wide proteomics community. One of the project’s key features is Python itself, an open source language increasingly popular in scientific programming. The main applications of the library are reproducible statistical data analysis and rapid software prototyping.

Pyteomics is hosted at the following sites:

Python package @ Python Package Index: http://pypi.python.org/pypi/pyteomics
project documentation @ python.org: http://packages.python.org/pyteomics
source code @ bitbucket: http://hg.theorchromo.ru/pyteomics
mailing list @ Google: https://groups.google.com/group/pyteomics

Feedback & Support

Please email to pyteomics@googlegroups.com with any questions about Pyteomics. You are welcome to use the BitBucket issue tracker to report bugs, request features, etc.

Required Python versions

Pyteomics supports Python 2.7 and Python 3. Python 2.6 and older are not supported.

Project dependencies

Pyteomics uses the following python packages:

numpy
matplotlib (used by pyteomics.pylab_aux)
lxml (used by pyteomics.mzml, pyteomics.pepxml, pyteomics.mzid)

GNU/Linux

The preferred way to obtain Pyteomics is via pip Python package manager. The shell code for a freshly installed Ubuntu system:

sudo apt-get install python-setuptools python-dev build-essential
sudo easy_install pip
sudo pip install lxml numpy matplotlib pyteomics

Windows

Download pre-compiled binary packages for Pyteomics dependencies:
- numpy
- matplotlib
- lxml
Download a pre-compiled binary Pyteomics package from the list.

If you have Enthought Python Distribution / ActivePython, execute in the command line:
```
easy_install pip
pip install lxml numpy matplotlib pyteomics
```

Project details

These details have not been verified by PyPI

Project links

Homepage

Release history Release notifications | RSS feed

4.7.5

Oct 18, 2024

4.7.4

Oct 1, 2024

4.7.3

Jul 30, 2024

4.7.2

Apr 26, 2024

4.7.1

Feb 14, 2024

4.7

Feb 5, 2024

4.6.3

Nov 1, 2023

4.6.2

Sep 7, 2023

4.6.1

Aug 31, 2023

4.6

Apr 20, 2023

4.5.6

Oct 31, 2022

4.5.5

Aug 21, 2022

4.5.4

Jul 18, 2022

4.5.3

Feb 23, 2022

4.5.2

Dec 16, 2021

4.5.1

Dec 10, 2021

4.5

Sep 20, 2021

4.4.2

Mar 26, 2021

4.4.1

Jan 14, 2021

4.4.0

Nov 16, 2020

4.4.0b0 pre-release

Nov 7, 2020

4.3.3

Sep 29, 2020

4.3.2

May 20, 2020

4.3.1

May 18, 2020

4.3

May 18, 2020

4.3a1 pre-release yanked

May 18, 2020

4.2

Feb 3, 2020

4.1.2

Jun 7, 2019

4.1.1

May 6, 2019

4.1

Mar 14, 2019

4.0.1

Jan 7, 2019

4.0

Jan 5, 2019

3.5.1

May 28, 2018

3.5

May 28, 2018

3.4.2

Jun 30, 2017

3.4.1

Feb 20, 2017

3.4

Sep 8, 2016

3.3.1

May 27, 2016

3.3

May 19, 2016

3.2

Feb 18, 2016

3.1.1

Oct 11, 2015

3.1

Sep 22, 2015

3.0.1

Apr 15, 2015

3.0.0

Apr 7, 2015

2.5.5

Jan 13, 2015

2.5.4

Jan 1, 2015

2.5.3

Dec 19, 2014

2.5.2

Nov 21, 2014

2.5.1

Oct 28, 2014

2.5.0

Oct 20, 2014

2.4.3

Jun 20, 2014

2.4.2

May 6, 2014

2.4.1

May 4, 2014

2.4.0

Apr 1, 2014

2.3.0

Feb 20, 2014

2.2.2

Dec 22, 2013

2.2.1

Nov 27, 2013

2.2.0

Oct 28, 2013

2.1.6

Sep 3, 2013

2.1.5

Apr 25, 2013

2.1.4

Apr 10, 2013

This version

2.1.3

Feb 26, 2013

2.1.2

Feb 1, 2013

2.1.1

Jan 27, 2013

2.1.0

Jan 14, 2013

2.0.3

Oct 23, 2012

2.0.2

Oct 4, 2012

2.0.1

Oct 4, 2012

2.0

Oct 3, 2012

1.2.5

Jun 17, 2012

1.2.4

Apr 25, 2012

1.2.3

Apr 18, 2012

1.2.2

Apr 10, 2012

1.2.1

Apr 7, 2012

1.2.0

Apr 5, 2012

1.1.0

Mar 9, 2012

1.0.0

Feb 14, 2012

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