Integrated analysis of Cross-platform MicroArray and Pathway data

Publications on InCroMAP

Please cite one of the following papers:

[1] Clemens Wrzodek. Inference and integration of biochemical networks with multilayered omics data. PhD thesis, University of Tuebingen, Tübingen, Germany, June 2013. [ details | link ]
[2] Clemens Wrzodek, Johannes Eichner, Finja Büchel, and Andreas Zell. InCroMAP: Integrated analysis of Cross-platform MicroArray and Pathway data. Bioinformatics, 29(4):506--508, December 2012. [ DOI | arXiv | details | link | pdf ]
[3] Clemens Wrzodek, Johannes Eichner, and Andreas Zell. Pathway-based visualization of cross-platform microarray datasets. Bioinformatics, 28(23):3021--3026, September 2012. [ DOI | arXiv | details | link | pdf ]
You can download these citations as BibTeX.

Brief overview

InCroMAP is a powerful, easy-to-use high-level cross-platform microarray dataset analysis tool. It smoothly integrates pathway and expression data analysis and bridges the gap between different microarray platforms and pathways. In general, InCroMAP is a tool for generic or pathway-based analysis and visualization of heterogeneous, cross-platform datasets.    

Some key features

  • Fast: Most reading, writing, visualization and analysis tasks are performed in a few seconds.
  • Up to date: Most required data is retrieved, cached and updated on-the-fly from web-APIs.
  • Platform independent: Tested on Windows, Linux, and Mac OS
  • Handsome: Clearly arranged user interface and nice pathway visualizations
  • Flexible: Currently supports mRNA, miRNA, DNA methylation and protein data.
  • All inclusive: Micro RNA target databases, identifier mapping files, etc. included.

Availability of InCroMAP

InCroMAP is available in two different forms:

  1. As a stand-alone application that visualizes and converts KGML files to various other file formats.
  2. As a webstart version, which directly runs with a single click.

Documentation for InCroMAP

You can download a comprehensive documentation for InCroMAP as PDF document.

Type Size Release date
User Guide [PDF] 2 MB 2012-09-28

Previous releases:
User Guide [PDF] 2 MB 2012-08-06
User Guide [PDF] 2 MB 2012-03-12

Screencasts for InCroMAP

Load mRNA data, perform a pathway enrichment analysis and visualize data in a pathway.

This short screencast shows how to import data into InCroMAP and perform a first analysis on this data. First, the required tabular input file format is presented, secondly this mRNA dataset is opened and lastly, an enrichment analysis is performed and the dataset is visualized in a pathway.
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