:: DESCRIPTION
DWD (Distance Weighted Discrimination) can perform systematic bias adjustment in microarray data.
::DEVELOPER
Dr. J. S. Marron in the Department of Statistics at University of North Carolina at Chapel Hill.
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Adjustment of Systematic Microarray Data Biases.
M. Benito, J. Parker, Q. Du, J. Wu, D. Xiang, C. Perou, J. Marron
Bioinformatics 20:105-144, 2004
:: DESCRIPTION
MPDA (Microarray Pooled DNA Analyzer) is an innovative tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data.
::DEVELOPER
Hsin-Chou Yang and Cathy SJ Fann(Institute of Biomedical Sciences, Academia Sinica, Taiwan)
:: SCREENSHOTS
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hsin-Chou Yang, Mei-Chu Huang, Ling-Hui Li, Chien-Hsing Lin, Alice L. T. Yu, Mitchell B. Diccianni, Jer-Yuan Wu, Yuarn-Tsong Chen, Cathy S. J. Fann (2008).
MPDA: Microarray Pooled DNA Analyzer.
BMC Bioinformatics. 9:196.
:: DESCRIPTION
M-BISON is a software to implement an efficient method for the integration of biological knowledge with microarray gene expression data to enhance identification of differentially expressed genes
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bernie J Daigle Jr and Russ B Altman
M-BISON: Microarray-based integration of data sources using networks
BMC Bioinformatics 2008, 9:214
:: DESCRIPTION
MPP (Microarray-to-Phylogeny-Pipeline) is a Java application, encompassing both new and established algorithms, for the analysis of gene and marker content datasets arising from high-throughput microarray techniques. MPP analyses flat file output from microarray experiments to determine the probability of the presence or absence of genes or markers within a genome. MPP can construct gene or marker content datasets for a number of genomes and can use the data to estimate an evolutionary tree or network. Results from gene content analyses may be validated by comparing them to known gene contents. MPP was initially developed to analyse data derived from comparative genome hybridization (CGH) microarray experiments in fungi and bacteria. It has recently been adapted to analyse retrotransposonbased insertion polymorphism (RBIP) marker scores derived from tagged microarray marker (TAM) experiments in pea. New analytical procedures may be added easily to MPP as plugins in order to increase the scope of the software.
::DEVELOPER
DICKS COMPUTATIONAL BIOLOGY GROUP
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Davey RP, Savva G, Dicks J and Roberts IN (2007)
MPP: A Microarray-To-Phylogeny Pipeline for Analysis of Gene and Marker Content Datasets.
Bioinformatics 23 (8): 1023-1025
:: DESCRIPTION
MAmodel is a microarray simulation model which can be used to validate different kinds of data analysis algorithms. The proposed model is unique in the sense that it includes all the steps that affect the quality of real microarray data. These steps include the simulation of biological ground truth data, applying biological and measurement technology specific error models, and finally simulating the microarray slide manufacturing and hybridization. After all these steps are taken into account, the simulated data has realistic biological and statistical characteristics.
::DEVELOPER
Computational Systems Biology Research group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
M. Nykter, T. Aho, M. Ahdesmäki, P. Ruusuvuori, A. Lehmussola, and O. Yli-Harja.
Simulation of microarray data with realistic characteristics.
BMC Bioinformatics, 7(349), 2006.
:: DESCRIPTION
Ginkgo is a spotted microarray data pre-processing platform featuring analysis functionalities for CGH (Comparative Genomic Hybridization) and expression data. This application provides a user-friendly graphical interface that allows viewing, analyzing, generating and reporting microarray data, easily and intuitively. Within the software there are a number of algorithms to address microarray data analysis needs, including normalization, filtering, data imputation, replicates merge, and expression statistical distribution tests.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
This application is released under the GPL v3 License: View License
Citation:
Quackenbush, J. Microarray data normalization and transformation. Nature Genetics. Vol.32 supplement pp496-501 (2002).
:: DESCRIPTION
Array Tools is a Microsoft Excel Add-In, which is designed to handle the import and export of Dictyostelium discoideum microarray data. It can be used to:
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Contact:
Ludwig Eichinger
Institut für Biochemie Köln, Zentrum Biochemie
University of Cologne
http://www.uni-koeln.de/med-fak/biochemie/transcriptomics/
:: DESCRIPTION
MAGIC Tool is an integrated microarray data analysis software.
The purpose of MAGIC Tool is to allow the user to begin with DNA microarray tiff files and end with biologically meaningful information. Comparative hybridization data (glass chips) and Affymetrix data are compatible with MAGIC Tool. You can start with tiff files or expression files.
MAGIC Tool allows the user to change parameters for clustering, data quantification etc.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Free software with open source.
Paper: MAGIC Tool: Integrated microarray data analysis (Bioinformatics, 2005)
:: DESCRIPTION
Venn Mapper is a program that cluster heterologous microarray data based on the number of co-occurring differentially expressed genes. The application loads microarray data (gene expression ratios) and determines which genes are up- or down-regulated by a user-defined ratio cut-off level. For each experiment, lists of differentially expressed genes are computed. Every list will be compared to every other list, and the number of co-occurring genes will be calculated. With the use of the binomial distribution, so called z-values can be assigned to the overlap found between two lists. The z-values can be directly imported into the Cluster and/or TreeView software.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
M. Smid ,L.C.J. Dorssers, G. Jenster, Venn Mapping: clustering of heterologous microarray data based on the number of co-occurring differentially expressed genes, Bioinformatics (2003) 19 (16): 2065-2071.
:: DESCRIPTION
ArrayMiner® is a set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data. Its unique graphical interface gives you an intimate understanding of the analysis and an easy publishing of its results.
ArrayMiner include clustering module & classmarking module.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
In order to be eligible for the free light version, your institution must be academic. The light version is limited to 500 genes and 10 experiments for the clustering module and 500 genes for the ClassMarker tool. The light licence’s validity is 1 year.
