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TM4 suite logo
a software for analyzing data from microarray experiments

TM4 is a suite of open source software tools (MADAM TIGR MIDAS MeV) that manage and analyze data from microarray experiments.

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BRB-ArrayTools logo

BRB-ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data.The array tools package utilizes an Excel front end.

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Magnolia logo

Since it has been an obligation to submit microarray experiment data to public repositories for publishing the experimental results, collecting and storing the data is an essential step in microarray study. Implemented with H2 DBMS as the backend storage, Magnolia provides PFGRC array users with a series of intelligent entry form to collect the information or parameters of experiment, bio-source, sample, probe, slide, scan, expression, and normalization, which is MIAME compliant (Minimal Informa

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ArrayMining logo

ArrayMining is a web-server for online automating microarray statistical analysis of gene and protein expression microarray data, designed as a supporting tool for investigation of the genetic components of diseases. By providing feature selection, clustering and prediction analysis, it performs five common gene expression analysis tasks:cross-study normalisation, feature selection, sample clustering, sample classification, network analysis, gene set analysis.

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Ginkgo logo

Ginkgo is a spotted microarray data pre-processing platform featuring analysis functionalities for CGH 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.

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AltAnalyze logo

AltAnalyze is an easy-to-use application for microarry and RNA-Seq analysis. For splicing sensitive platforms, AltAnalyze will assess alternative exon expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for conventional arrays (RMA summarization, QC, statistics, annotation, clustering, lineage characterization and gene-set enrichement).

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Gene Cruiser logo
Gene Cruiser allows: Broad

GeneCruiser provides integrated access to the gene and microarray feature information freely available from public databases. It allows users to retrieve annotations from various databases (LocusLink, RefSeq, SwissProt) using Affymetrix probe identifiers, or convert genes from accession numbers or keywords into matching probe IDs on one or more microarray chips. GeneCruiser is a web service accessible through a web interface, and is also available as a GenePattern module

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Integrative Array (iArray) Analyzer logo

iArray is a data mining and visualization software platform for the integrative analysis of multiple cross-platform microarray datasets under Windows XP.

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NetAffx logo

The NetAffx™ Analysis Center enables researchers to correlate their GeneChip® array results with array design and annotation information.

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SNP Filter Scripts logo

Scripts for Filtering Raw SNP calls from Affymetrix GeneChip® Resequencing Chips We have developed a set of scripts to identify and remove false positive SNP calls that are present in the CHP files produced by the Affymetrix GSEQ software. These scripts are described in an online presentation available here, and are described more completely in a published manuscript (Nucleic Acids Research 2007; doi: 10.1093/nar/gkm918). These scripts have been designed to work in our processing environment.

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ScanAlyze logo

Process fluorescent images of microarrays. Includes semi-automatic definition of grids and complex pixel and spot analyses. Outputs to tab-delimited text files for transfer to any database.

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Gene Set Enrichm Analysis (GSEA) logo

The GSEA algorithm implemented in MeV is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). GSEA software uses the Molecular Signatures Database (MSigDB), a collection of annotated gene sets.

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Bioconductor logo

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language and most bioconductor components are distributed as R packages, which are add-on modules for R. It is open source and open development. Boconductor core team is based primarily at the Fred Hutchinson Cancer Research Center (http://en.wikipedia.org/wiki/Bioconductor)

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