Web app
Genevestigator Genevestigator

Genevestigator

An innovative online platform to help you interpret your results, prioritize…

An innovative online platform to help you interpret your results, prioritize targets and biomarkers, identify correlated genes, discover novel disease-specific genes, or simply to explore the…

Desktop app
G T A T C G C T A RobiNA RobiNA

RobiNA

A User Friendly Graphical Interface to Powerful Open Source Microarray and…

A User Friendly Graphical Interface to Powerful Open Source Microarray and RNA-Seq Processing.

Web app
INCLUSive INCLUSive

INCLUSive

A suite of algorithms and tools for the analysis of gene expression data and…

A suite of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements. The tools allow normalization, filtering and clustering of microarray…

Desktop app
BRB-ArrayTools BRB-ArrayTools

BRB-ArrayTools

An integrated package for the visualization and statistical analysis of DNA…

An integrated package for the visualization and statistical analysis of DNA microarray gene expression data.

Web app
EMMA EMMA

EMMA

A web-based system for management and analysis of transcriptomic data. EMMA 2…

A web-based system for management and analysis of transcriptomic data. EMMA 2 allows mapping of gene expression data onto proteome data or pathways and vice versa. It provides extensible analysis and…

Web app
NIA Array Analysis NIA Array Analysis

NIA Array Analysis

A program for microarray data analysis, which features the false discovery rate…

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…

Desktop app
J-Express J-Express

J-Express

An application to analyze gene expression (microarray) data in a flexible way…

An application to analyze gene expression (microarray) data in a flexible way giving access to multidimensional scaling, clustering, and visualization methods. J-Express includes implementations of…

Web app
ArrayPipe ArrayPipe

ArrayPipe

Allows the automated application of complex analyses to microarray data which…

Allows the automated application of complex analyses to microarray data which can range from single slides to large data sets including replicates and dye-swaps. It handles output from most commonly…

Desktop app
Integrated analysis… Integrated analysis of Cross-platform MicroArray…

InCroMAP Integrated analysis of Cross-platform MicroArray and Pathway data

A tool for the analysis and visualization of high-level microarray data from…

A tool for the analysis and visualization of high-level microarray data from individual or multiple different platforms. Currently, InCroMAP supports mRNA, microRNA, DNA methylation and protein…

Web app
ArrayTrack ArrayTrack

ArrayTrack

A Food and Drug Administration (FDA) bioinformatics tool that has been widely…

A Food and Drug Administration (FDA) bioinformatics tool that has been widely adopted by the research community for genomics studies. It provides an integrated environment for microarray data…

Web app
Remote Analysis… Remote Analysis Computation for gene Expression…

RACE Remote Analysis Computation for gene Expression data

Offers an easy to use collection of bioinformatics web tools to analyze DNA…

Offers an easy to use collection of bioinformatics web tools to analyze DNA microarray data, without requiring any installation or maintenance on the user side. By using various R subroutines and…

Web app
GenePublisher GenePublisher

GenePublisher

A system for automatic analysis of data from DNA microarray experiments. Raw…

A system for automatic analysis of data from DNA microarray experiments. Raw data are uploaded to the server together with a specification of the data. The server performs normalization, statistical…

Web app
WebArrayDB WebArrayDB

WebArrayDB

Offers a convenient platform for bench biologists to access several…

Offers a convenient platform for bench biologists to access several cutting-edge microarray data analysis tools. Microarray analysis using WebArray can be executed in three steps: 1) uploading and…

Web app
Multi-Conditional… Multi-Conditional Hybridization Intensity…

M-CHiPS Multi-Conditional Hybridization Intensity Processing System

A data warehousing concept, focuses on providing both structure and algorithms…

A data warehousing concept, focuses on providing both structure and algorithms suitable for statistical analysis of a microarray database's entire contents including the experiment annotations.…

Web app
Asterias Asterias

Asterias

An open-source, web-based, suite for the analysis of gene expression and aCGH…

An open-source, web-based, suite for the analysis of gene expression and aCGH data. Asterias implements validated statistical methods, and most of the applications use parallel computing, which…

Web app
Exon Array Analyzer Exon Array Analyzer

EAA Exon Array Analyzer

Provides a user-friendly interface to identify alternative splicing events…

Provides a user-friendly interface to identify alternative splicing events analyzed with Affymetrix Exon Arrays. The EAA implements the Splice Index algorithm to identify differential expressed…

Web app
Gene Array Analyzer Gene Array Analyzer

GAA Gene Array Analyzer

A versatile tool to analyze GeneChip Array data at both gene and exon levels.…

A versatile tool to analyze GeneChip Array data at both gene and exon levels. Gene arrays were originally designed to measure genome-wide expression changes. However, their probe design also allows…

Desktop app
Functional Genomics… Functional Genomics Data Pipeline

FGDP Functional Genomics Data Pipeline

A Java-based, Microarray or Genechip data analysis system.

A Java-based, Microarray or Genechip data analysis system.

Desktop app
Gecko Gecko

Gecko

A complete, high-capacity centralized gene expression analysis system,…

A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.

Desktop app
G T A T C G C T A Guide Guide

Guide

A desktop application for the bench biologists to analyse RNA-Seq and…

A desktop application for the bench biologists to analyse RNA-Seq and microarray expression data.

Desktop app
Gene Expression Open… Gene Expression Open Source System

GEOSS Gene Expression Open Source System

A complete system used to store and analyze gene expression data.

A complete system used to store and analyze gene expression data.

Desktop app
PIPE-chipSAD PIPE-chipSAD

PIPE-chipSAD

Integrates the analysis of the hybridization signal with the genomic position…

Integrates the analysis of the hybridization signal with the genomic position of probes and identifies portions of the genome transcribing for mRNAs. PIPE-chipSAD is a pipeline for bacterial…

Web app
noncoder noncoder

noncoder

Analyzes Affymetrix GeneChip Exon 1.0 ST arrays (exon arrays) for expression…

Analyzes Affymetrix GeneChip Exon 1.0 ST arrays (exon arrays) for expression changes of long non-coding RNAs (lncRNAs). noncoder provides the detailed annotation information of lncRNAs. It is…

Desktop app
Robin Robin

Robin

Harnesses the advanced statistical analysis functions of the R/BioConductor…

Harnesses the advanced statistical analysis functions of the R/BioConductor project. Robin implements streamlined workflows that guide the user through all steps of two-color, single-color, or…

Web app
Comprehensive R-based… Comprehensive R-based Microarray Analysis web…

CARMAweb Comprehensive R-based Microarray Analysis web service

Provides several unique features in a modular and flexible system for the…

Provides several unique features in a modular and flexible system for the analysis of microarray data. The design and modular conception of CARMAweb allows the use of the different analysis modules…

Desktop app
EXpression Analyzer… EXpression Analyzer and DisplayER

EXPANDER EXpression Analyzer and DisplayER

An integrated software platform for the analysis of microarray gene expression…

An integrated software platform for the analysis of microarray gene expression data. EXPANDER is designed to support all the stages of microarray data analysis, from raw data normalization to…

Desktop app
maigesPack maigesPack

maigesPack

Uses functions of various other packages together with other functions in a…

Uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data. maigesPack helps with the data organization and also with the…

Desktop app
Transcriptome… Transcriptome Analysis Console Software

TAC Software Transcriptome Analysis Console Software

Enables you to go beyond simple identification of differentially expression by…

Enables you to go beyond simple identification of differentially expression by providing visualizations of complex gene pathway networks, miRNA and target gene interactions, and alternative splicing…

Desktop app
MicroArray ANalysis… MicroArray ANalysis Of VAriance

R/maanova MicroArray ANalysis Of VAriance

An extensible, interactive environment for microarray analysis. R/maanova…

An extensible, interactive environment for microarray analysis. R/maanova provides a complete work flow for microarray data analysis including: 1) data quality checks and visualization, 2) data…

Web app
ExonMiner ExonMiner

ExonMiner

A web service for analysis of exon array data to detect transcripts that have…

A web service for analysis of exon array data to detect transcripts that have significantly different splicing patterns in two cells, e.g. normal and cancer cells. ExonMiner can perform the following…

Desktop app
Qlucore Omics Explorer Qlucore Omics Explorer

Qlucore Omics Explorer

A next-generation bioinformatics software that combines powerful statistical…

A next-generation bioinformatics software that combines powerful statistical methods with real time visualization and an intuitive user interface.

Web app
ArrayMining ArrayMining

ArrayMining

A server for automatic analysis of DNA microarray data, providing cross-study…

A server for automatic analysis of DNA microarray data, providing cross-study normalisation, feature selection, clustering, prediction, co-expression network analysis and gene set analysis.

Desktop app
Eureka-DMA Eureka-DMA

Eureka-DMA

A user-friendly software that comprises a set of methods for the interpretation…

A user-friendly software that comprises a set of methods for the interpretation of gene expression arrays.

Web app
Multi Experiment… Multi Experiment Matrix

MEM Multi Experiment Matrix

A web resource for gene expression similarity searches across many datasets.…

A web resource for gene expression similarity searches across many datasets. Unique features include automatic detection, characterization and visualization of datasets that includes the strongest…

Web app
Automated Microarray… Automated Microarray Pipeline

AMP Automated Microarray Pipeline

Its purpose is to provide a means of normalization and analysis of microarray…

Its purpose is to provide a means of normalization and analysis of microarray data.

Desktop app
Simpleaffy Simpleaffy

Simpleaffy

Provides access to a variety of QC metrics for assessing the quality of RNA…

Provides access to a variety of QC metrics for assessing the quality of RNA samples and of the intermediate stages of sample preparation and hybridization. Simpleaffy also offers fast implementations…

Desktop app
ArrayTools ArrayTools

ArrayTools

A package designed to provide solutions for quality assessment and to detect…

A package designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays.…

Desktop app
limmaGUI limmaGUI

limmaGUI

A graphical user interface (GUI) based on R-Tcl/Tk for the exploration and…

A graphical user interface (GUI) based on R-Tcl/Tk for the exploration and linear modeling of data from two-color spotted microarray experiments, especially the assessment of differential expression…

Desktop app
AffyExpress AffyExpress

AffyExpress

The purpose of this package is to provide a comprehensive and easy-to-use tool…

The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.

Desktop app
affylmGUI affylmGUI

affylmGUI

A Graphical User Interface for affy analysis using the limma Microarray package.

A Graphical User Interface for affy analysis using the limma Microarray package.

Desktop app
oneChannelGUI oneChannelGUI

oneChannelGUI

A graphical interface designed to facilitate analysis of microarrays and…

A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops. oneChannelGUI can be used for quality control, normalization, filtering, statistical validation…

Web app
G T A T C G C T A expressionplot expressionplot

expressionplot

A software package consisting of a default back end, which prepares raw…

A software package consisting of a default back end, which prepares raw sequencing or Affymetrix microarray data, and a web-based front end, which offers a biologically centered interface to browse,…

Desktop app
Gene ARMADA Gene ARMADA

Gene ARMADA

A MATLAB implemented platform with a GUI, integrating all steps of microarray…

A MATLAB implemented platform with a GUI, integrating all steps of microarray data analysis including automated data import, noise correction, filtering, normalization, statistical testing,…

Desktop app
G T A T C G C T A Array Studio Array Studio

Array Studio

Provides the premier enterprise solution for data content, framework and…

Provides the premier enterprise solution for data content, framework and graphical user interface for omic and next-generation sequencing data analysis. Array Suite (Array Studio and Array Server)…

Desktop app
GeneSpring GX GeneSpring GX

GeneSpring GX

Provides powerful, accessible statistical tools for fast visualization and…

Provides powerful, accessible statistical tools for fast visualization and analysis of microarrays - expression arrays, miRNA, exon arrays and genomics copy number data.

Desktop app
GenomeStudio GenomeStudio

GenomeStudio

Visualize and analyze data generated on Illumina array platforms. GenomeStudio…

Visualize and analyze data generated on Illumina array platforms. GenomeStudio supports the primary analysis of microarray data. Performance-optimized tools and a user-friendly graphical interface…

Desktop app
Genedata Expressionist Genedata Expressionist

Genedata Expressionist

A comprehensive, enterprise software solution that manages, analyzes, and…

A comprehensive, enterprise software solution that manages, analyzes, and visualizes massive amounts of raw data from next-generation sequencing, microarray and other genomic technologies.

Web app
ArrayQuest ArrayQuest

ArrayQuest

Enables browser-based implementation of DNA microarray data analysis programs…

Enables browser-based implementation of DNA microarray data analysis programs that can be executed on a Linux-based platform. Key features of ArrayQuest are that (1) it is capable of executing…

Desktop app
GAAS GAAS

GAAS

An integrated software framework for efficient management, analysis and…

An integrated software framework for efficient management, analysis and visualization of large amounts of gene expression data across replicated experiments.

Web app
A A A Gene-set activity… Gene-set activity toolbox

GAT Gene-set activity toolbox

A comprehensive gene expression analysis tool that is implemented with data…

A comprehensive gene expression analysis tool that is implemented with data retriever, traditional data pre-processing, several gene-set analysis methods, network visualization and data mining tools.…

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