Microarray

Microarray Explorer (MAExplorer) is a Java microarray data-mining bioinformatics program. It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user written MAEPlugins, documentation, tutorials, demo data. Platforms: Windows, Mac, Solaris, Linux

PheMaDB is a web-based data management system to store and analyze OmniLog Phenotype Microarray data. The manuscript can be accessed here: http://www.biomedcentral.com/1471-2105/12/109. Chang WE et al. BMC Bioinformatics. 2011 Apr 20;12(1):109. Platforms: Mac

MeV or Multiple Experiment Viewer is a Java tool to help you with microarray gene expression data analysis. MeV supports 5 input formats, and provides an intuitive graphical interface for clustering, classification, statistical analysis and theme discovery. Platforms: Windows

MeV or Multiple Experiment Viewer is a Java tool to help you with microarray gene expression data analysis. MeV supports 5 input formats, and provides an intuitive graphical interface for clustering, classification, statistical analysis and theme discovery. Platforms: Mac

The Integrated Genome Browser (IGB, pronounced Ig-Bee) is an interactive, zoomable, scrollable software program you can use to visualize and explore genome-scale data sets, such as tiling array data, next-generation sequencing results, genome annotations, microarray designs, and the sequence... Platforms: Windows

GNomEx is Genomic LIMS and Analysis Project Center designed by the Huntsman Cancer Institute for use by microarray and next generation sequencing core facilities and large research laboratories. KWs: Illumina, Affymetrix, Agilent, MAGE, MySQL/Flex... Platforms: Windows

The application loads microarray data (gene expression ratios) and determines which genes are up- or downregulated 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... Platforms: Windows

MEFIT, also known as the Microarray Experiment Functional Integration Technology is developed as a system for microarray integration. Given any amount of microarray data, it predicts the probability of pairwise functional relationship for any gene pair within individual biological functions.... Platforms: Windows

In one type of gene expression analysis, fluorescently tagged messenger RNA from different cells are hybridized to a microscopic array of thousands of complimentary DNA spots that correspond to different genes. Illuminated spots emit different color light, indicating which genes are expressed... Platforms: Matlab

The CMVE toolbox estimates missing values by using correlation structure of the data. The software can be used to impute missing values in any correlated data especally microarray gene expression data. The imputation performance of the software has proven significant affect on gene regulatory... Platforms: Matlab

PhenoDB is a web-based data management system to store and analyze OmniLog Phenotypic Microarray data. Platforms: PHP

StepMiner is a new method for analyzing time course microarray data that extracts transitions between two states, up-regulated and down-regulated. For each gene, StepMiner reports the model that best matches its behavior. The models are sequences of one or two transitions. The rising or falling... Platforms: Mac

Cscape is an application for visualizing and navigating through data from a Reverse Phase Protein Microarray (RPMA). Cscape uses the Google Maps API to map the RPMA data on top of an image of a cancer cell and its associated pathways. Platforms: *nix

AlleleID is a comprehensive desktop tool designed to address the challenges of pathogen detection, bacterial identification or taxa/species discrimination using microarrays and TaqMan® and molecular beacon qPCR assays. With ClustalW multiple sequence alignment at its core, AlleleID can design... Platforms: Mac

In order to facilitate standardization and exchange of microarray layout, this project provides an ADF (Array design File))/MAGE-ML converter. Platforms: Windows, Mac, Linux

AnnTools is an efficient, fast and robust bioinformatics tool annotating SNP and CNV calls generated from sequencing and microarray data. Platforms: Mac, BSD, Linux

Tab2MAGE uses a flexible spreadsheet format for MIAME annotation of microarray experiments. Tab2MAGE spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange. Platforms: Windows, Mac, Linux

ArrayPlex integrates various forms of microarray data from diverse annotation and primary data sources. It provides a programmatic framework (API set) for collaborative development and deploys as easy to maintain client-server architecture. Platforms: Windows, Mac, BSD, Linux

AutoMATRIX is a tool to predict key transcription factors in microarray experiments. Platforms: Windows, Mac, Linux

This is a collection of ImageJ macros (scripts) for performing color deconvolution and analysis of immunohistochemistry (IHC) staining on tissue microarray (TMA) images Platforms: Windows, Mac, Linux