**Professor Pedro Mendes
Computational Systems Biology**

**Software for Multivariate Data Analysis for Genomics and Systems Biology**

**Ometer** is software for multivariate analysis of functional genomics and systems biology data (it can be used for other types of data, too). **Ometer** is driven by a plain command line interface, which allows it to be called directly from scripts. **Ometer** is focused on efficient calculation of numerical results, which are written to tab-delimited files. Files are produced for visualization with gnuplot and graphviz, as well as reports formated in HTML.

- correlation analysis
- partial correlation analysis
- principal component analysis (PCA), including biplot display
- linear multiple discriminant analysis (MDA),
- linear multiple discriminant analysis with genetic algorithm variable selection - 2 different algorithms (GA-DFA and GA-DFA2).
- non-negative matrix factorization (NMF)
- factor analysis with varimax rotation (FA)

ometer-0.60.tar.gz (source code 300.22 Kb)

To install, first download this file and untar it. Then run *./configure && make && make install*, this will put *ometer* in */usr/local/bin*. If you need to install ometer in other location, do instead *./configure --prefix=yourpath && make && make install*.

version 0.60 for windows (1.92 Mb)

To install the windows version: download the executable file an save it in any folder that is in your path (eg C:\WINDOWS). If you are not able to do so, then put it in a new folder and change your path to include that folder (right-click on *My Computer*, select *Properties*, *Advanced*, and click on *Environment Variables*, then add it to the PATH variable) .

version 0.60 executable binary for Linux on Pentium4 (4.23 Mb)

To install **only on a Intel 32 bit processor**. Put this executable file on your path and change its the permissions to executable (*chmod a+x ometer*). Note that this will not run on other processors (eg on AMD). If you need to install and run on other processors, you should build ometer from source code.

- File formats
- File transformations
- Correlation analysis
- Principal Components Analysis - PCA
- Linear Multiple Discriminant Analysis - MDA
- Linear Multiple Discriminant Analysis with GA Variable Selection - GA-DFA

Other documentation to appear later:

- Non-negative matrix factorization
- Factor analysis
- partial correlation analysis
- Producing plots of ometer results with gnuplot
- Producing correlation graphs with graphviz

**Ometer** was written by Pedro Mendes. The partial correlation algorithm was developed by Alberto de la Fuente. Other credits:

- CLO++, a command line option parser generator.
- LAPACK and BLAS routines for matrix algebra
- some binary versions include the Intel MKL version of LAPACK
- DCDFLIB, a library of comulative distribution functions, by Barry Brown, James Lovato, and Kathy Russell
- The C++ Standard Template Library, for data structures and algorithms
- MDA code based on original by F. Murtagh <murtagh@scivax.stsci.edu>, Munich, Jan 1986

This Website by Pedro Mendes is licensed under a Creative Commons Attribution 4.0 International License. This page uses the Perfect 'Left Menu' 2 Column Liquid Layout.