ChromA 0.9 – Alignment for Chromatography Mass Spectrometry Data

ChromA 0.9

:: DESCRIPTION

ChromA (Chromatogram Alignment) provides the Dynamic Time Warping algorithm for the alignment of data from the domain of Gas- and Liquid-Chromatography Mass-Spectrometry. It uses additional constraints and can be configured to use different local functions to evaluate the similarity of mass spectra between chromatograms. It allows the definition of anchors, which are the positions of conserved compounds, constraining the alignment and providing a speedup. Furthermore, ChromA provides different visualizations of the alignment, as well as a textual format for further processing of chromatograms.

::DEVELOPER

Nils Hoffmann

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac / Windows
  • Java

:: DOWNLOAD

ChromA

:: MORE INFORMATION

Citation

ChromA: Signal Based Retention Time Alignment for Chromatography-Mass Spectrometry Data
Nils Hoffmann; Jens Stoye
Bioinformatics 2009; doi: 10.1093/bioinformatics/btp343

GenePublisher 1.03 – Analysis of DNA Microarray Data

GenePublisher 1.03

:: DESCRIPTION

GenePublisher performs automated data analysis from gene expression experiments on a number of different platforms. This server accepts gene tables or Affymetrix CEL files as input, performs numerical and statistical analysis, links the results to various databases, and returns a report of the results. The input data is deleted immediately upon completion of the analysis unless you select the database option below.

::DEVELOPER

CBS (Center for Biological Sequence Analysis) at Technical University of Denmark

:: SCREENSHOTS

:: REQUIREMENTS

  • web browser

:: MORE INFORMATION

Input restrictions:

  • The input CEL files must be compressed with gzip (available from www.gzip.org) and cannot be more than 30 Mbytes in total size. That corresponds to 12 HuGeneFL chips, 10 HG_U95A chips, 22 Focus chips, 8 HG-U133A chips, and so on. The maximum number of chips accepted on this web server is currently 12. There is another server without input restrictions.
  • Avoid using characters _, &, %, # in the input as they may interfere with analysis.

For publication of results, please cite:

GenePublisher: Automated Analysis of DNA Microarray Data.
Knudsen, S., Workman, C., Sicheritz-Ponten, T., and Friis, C.
Nucleic Acids Research. Vol. 31, No. 13 3471-3476.

AMIADA 2.0.7 – Analysis of Microarray Data

AMIADA 2.0.7

:: DESCRIPTION

AMIADA is an integrated computer program for organizing, exploring, visualizing, and analyzing microarray data. It features an EXCEL-like user interface and performs data transformation, principal component analysis, a variety of cluster analysis and extensive graphic functions for visualizing expression profiles.

::DEVELOPER

Dr. Xuhua Xia

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

AMIADA

:: MORE INFORMATION

Citation : Xia, X., and Xie. Z., 2001 AMADA: Analysis of microarray data. Bioinformatics 17:569-570.