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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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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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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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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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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MicroArray Genome Imaging and Clustering Tool (MAGIC Tool)
Category: DNA microarray software
MAGIC Tool is an integrated microarray data analysis free software with open source.
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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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