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Bionconductor (http://www.bioconductor.org/): Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology. Bioconductor is based primarily on the statistical R programming language, but does contain contributions in other programming languages.
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Affy (https://www.rdocumentation.org/packages/affy/versions/1.50.0) and Simpleaffy (https://www.bioconductor.org/packages/release/bioc/html/simpleaffy.html): packages of R Documentation. Affy package contains functions for exploratory oligonucleotide array analysis. Simpleaffy provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like.
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SAM (https://statweb.stanford.edu/~tibs/SAM/): Significant Analysis of Microarray assigns a score to each gene on the basis of change in gene expression relative to the standard deviation of repeated measurements.
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starScan: an integrated web-based tool for scanning sRNA targets using degradome sequencing data from 20 species. Given a sRNA sequence from plants or animals, StarScan performs an ultrafast and exhaustive search for potential sRNA–target interactions in annotated and unannotated genomic regions. The interactions between small RNAs and target transcripts were further evaluated using alignScore.
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ArrayVision (https://www.biocompare.com/Product-Reviews/41169-ArrayVision-Version-8-0/): can be used to analyze arrays with fluorescent, radio-isotopic and chemiluminescent content with specific analysis protocol templates for each type. The analysis wizard in the software is particularly useful when designing the analysis parameters. There is a specific analysis template for the fluorescent, radio-isotopic and chemiluminescent signal array types with sub-types of expression, comparative expression, screening and protein analysis available for each signal type.
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Array-Pro Analyzer: microarray and high-density array image analysis software designed for the molecular biologist. This automated software provides a range of image analysis tools to achieve maximum signal to noise, repeatability, and quantitative accuracy.
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J-Express (https://www.mybiosoftware.com/j-express-2009-analysis-visualization-microarray-data.html): a comprehensive portable software package for analysis and visualization of microarray data. The software gives access to methods for unsupervised analysis (clustering etc.), supervised analysis (SAM, Feature Subset Selection, etc.) and visualisation in an integrated and flexible way.
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MAExplorer (http://maexplorer.sourceforge.net/): Microarray Explorer is a Java-based data-mining facility for cDNA or oligonucleotide microarray databases. It may be downloaded and run as a stand-alone application on your computer. Its exploratory data analysis environment provides tools for the data-mining of quantitative expression profiles across multiple microarrays.
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dChip (https://sites.google.com/site/dchipsoft/home): analysis and visualization of gene expression and SNP microarrays.
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BRB-ArrayTools (https://brb.nci.nih.gov/BRB-ArrayTools/): an integrated package for the visualization and statistical analysis of Microarray gene expression, copy number, methylation and RNA-Seq data.
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GalFileGenerator: Conversion of a file of 96 well plates into a file of 384 well plates, and conversion of a file of 384 well plates into an Axon GenePix Gene Array List file (.gal file).
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GenMAPP-CS: an open-source software for pathway visualization and analysis, bringing the intuitive and easy-to-use features of GenMAPP to the powerful and flexible Cytoscape platform.
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MADAM (https://www.mybiosoftware.com/madam-4-1-microarray-data-manager.html): MicroArray DAta Manager is a suite of tools used to upload,download, and display a plethora of microarray data to and from a database management system (MySql).
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Spotfinder: a multi-channel image analysis tool designed for the rapid, reproducible, user-aided analysis of microarray images and the quantification of gene expression.
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MIDAS: Microarray Data Analysis System is an application that allows users to perform normalization and other statistical data analysis, trim the raw experimental data, and create output for MeV.
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WebMeV (http://mev.tm4.org/#/welcome): Multiple Experiment Viewer is a cloud-based application supporting analysis, visualization, and stratification of large genomic data, particularly for RNASeq and microarray data.
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Java Treeview: An Open Source, Extensible Viewer for Microarray Data in the PCL or CDT format.
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EXPANDER: EXpression Analyzer and DisplayER is a java-based tool for the analysis of gene expression data.
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OligoArray (http://berry.engin.umich.edu/oligoarray2_1/): a software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction.
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BAGEL: Bayesian Analysis of Gene Expression Levels, statistical quantification of relative mRNA level across multiple strains or treatments.
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CAGED: Cluster Analysis of Gene Expression Dynamics is a computer program for the analysis of temporal gene expression data. CAGED is based on Bayesian Clustering by Dynamics, a method that identifies the most probable set of clusters given a set of time series.
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GAAS (http://www.bioinformatics.deib.polimi.it/GAAS/GAAS-fig.asp): gene array analyzer software for management, analysis and visualization of gene expression data.
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NIA Array Analysis Tool (https://lgsun.grc.nia.nih.gov/ANOVA/): a program for microarray data analysis, which features the false discovery rate for testing statistical significance and the principal component analysis using the singular value decomposition method for detecting the global trends of gene-expression patterns.
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UCSF Spot: a program for microarray image quantification.
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ArrayMiner: a set of analysis tools using advanced algorithms to reveal the true structure of gene expression data.
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Venn Mapper (http://www.mybiosoftware.com/venn-mapper-1-01-compare-heterologous-microarray-data-sets.html): a program that clusters heterologous microarray data based on the number of co-occurring differentially expressed genes.
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MAGIC Tool (https://www.mybiosoftware.com/magic-tool-2-1-microarray-genome-imaging-clustering-tool.html): an integrated microarray data analysis software.
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Mayday (http://www.mybiosoftware.com/mayday-2-11-microarray-data-analysis.html): a workbench for visualization, analysis and storage of microarray data.
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ChipInspector (https://www.mybiosoftware.com/chipinspector-2-1-microarray-data-analysis.html): genomatix tool for high quality microarray data analysis. Based on single probes instead of probe sets results of superior significance can be retrieved in combination with the Genomatix genome annotation. Expression levels can be assigned not only to genes but to separate (alternative) transcripts.
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OligoWiz (http://www.cbs.dtu.dk/services/OligoWiz/index.before_takedown.php): this server performs intelligent design of oligonucleotides for DNA microarrays.
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PermutMatrix: a work space to graphically explore gene expression data.
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KegArray: provides an environment for analyzing both transcriptome data (gene expression profiles) and metabolome data (compound profiles). KegArray is a Java application that enables users to easily map those data to KEGG resources including PATHWAY, BRITE and genome maps.
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Picky: an optimal oligo microarray design program that identifies probes that are very unique and specific to input sequences based on thermodynamic calculations.
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ParaSAM (https://bio.tools/parasam): a high performance parallel processing implementation of the SAM (Significance Analysis of Microarrays) algorithm.
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COCAS (https://www.mybiosoftware.com/cocas-2-4-chip-chip-analysis-suite.html): a standalone Chromatin immunoprecipitation microarray (ChIP-on-chip) analysis application.
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ArrayCluster (https://www.ism.ac.jp/~higuchi/arraycluster.htm): a software to perform the mixed factors analysis of microarray gene expression data.
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Array Designer (http://www.premierbiosoft.com/dnamicroarray/): a microarray software for fast, efficient design of specific oligos for making whole genome arrays, tiling arrays and resequencing arrays.
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