Welcome to the PyChem homepage

PyChem is no longer under development

This website hosts the PyChem(Python and Chemometrics) package for univariate and multivariate data analysis, the project is hosted at Sourceforge, where further details can be found at the PyChem page.

How to cite PyChem: Jarvis, R.M.; Broadhurst, D.; Johnson, H.E.; O'Boyle, N. & Goodacre, R. (2006) PyChem - a multivariate analysis package for Python. Bioinformatics 22(20):2565-2566. [download pdf here]

PyChem Modules

  • Storage of supporting data (metadata)

  • Interactive user defined calculation of peak metrics (areas, intensities etc)

  • Univariate tests; analysis of variance (ANOVA), Kruskal-Wallis, Correlation Coefficient

  • Spectral pre-processing: scaling, filtering, baseline correction, derivatisation, extended multiplicative scatter correction (EMSC)

  • Principal components analysis for data visualisation and dimensionality reduction

  • Discriminant function analysis (DFA, also known as canonical variates or correlation analysis - CVA, CCA)

  • Cluster analysis - including K-means and hierarchical clustering

  • Partial least squares (PLS) regression (PLS1 & PLS2) and PLS - discriminant analysis

  • Genetic algorithm based variable selector coupled to PLS and DFA


This was a rapid application development (RAD) using:

Python 2.5, an interpreted, interactive, object-oriented programming language. It is often compared to Ruby, Tcl, Perl, Scheme or Java

Boa Constructor 0.6.1, A RAD GUI building IDE for wxPython

wxPython 2.8, a C++ framework providing GUI (Graphical User Interface) and other facilities on more than one platform

SciPy/NumPy 0.6.0
, an open source library of scientific tools for Python.

PyCluster through Biopython, an extension module to Python for the C Clustering Library

The Tango Desktop Project, exists to help create a consistent graphical user interface experience for free and Open Source software

Py2exe, converts python scripts into standalone windows programs

Inno Setup, creates windows installers for program distribution