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Bioinformatics workflows | Gene expression microarray data analysis

Genevestigator
Web

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…

G T A T C G C T A
AltAnalyze
Desktop

AltAnalyze

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis.…

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess…

limmaGUI
Desktop

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…

Simpleaffy
Desktop

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…

G T A T C G C T A
RobiNA
Desktop

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.

oneChannelGUI
Desktop

oneChannelGUI

Facilitates analysis of microarrays and miRNA/RNA-seq data on laptops.…

Facilitates analysis of microarrays and miRNA/RNA-seq data on laptops. oneChannelGUI can be used for quality control, normalization, filtering, statistical validation and data mining for single…

InCroMAP
Desktop

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…

MEM
Web

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…

EMMA
Web

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…

ArrayTrack
Web

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…

ArrayPipe
Web

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…

RACE
Web

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…

J-Express
Desktop

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…

NIA Array…
Web

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…

affylmGUI
Desktop

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.

GenePublisher
Web

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…

Asterias
Web

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…

BRB-ArrayTools
Desktop

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.

MMAD
Desktop

MMAD Microarray Microdissection with Analysis of Differences

Performs robust tissue microdissection in silico, and improves the detection of…

Performs robust tissue microdissection in silico, and improves the detection of differentially expressed genes. MMAD is a computational approach that (i) allows for simultaneous estimation of cell…

GAA
Web

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…

M-CHiPS
Web

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.…

Enumerateblood
Desktop

Enumerateblood

Exposes a statistical model capable of accurately inferring the composition of…

Exposes a statistical model capable of accurately inferring the composition of peripheral whole blood samples from Affymetrix Gene ST expression profiles. The strategy adopted to derive…

EAA
Web

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…

WebArrayDB
Web

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…

noncoder
Web

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…

CARMAweb
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…

PIPE-chipSAD
Desktop

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…

EXPANDER
Desktop

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…

FGDP
Desktop

FGDP Functional Genomics Data Pipeline

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

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

Gecko
Desktop

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.

ArrayQuest
Web

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…

Gene ARMADA
Desktop

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,…

GAAS
Desktop

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.

maigesPack
Desktop

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…

GEOSS
Desktop

GEOSS Gene Expression Open Source System

Stores and analyzes gene expression data. GEOSS is an open source gene…

Stores and analyzes gene expression data. GEOSS is an open source gene expression data management system that provides a relational database, a web interface, and an analysis suite. This resource is…

G T A T C G C T A
Guide
Desktop

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.

MARS
Web

MARS Microarray Analysis and Retrieval System

Provides a comprehensive MIAME (Minimum Information About a Microarray…

Provides a comprehensive MIAME (Minimum Information About a Microarray Experiment) supportive suite for storing, retrieving, and analyzing multi-color microarray data. MARS comprises a laboratory…

Robin
Desktop

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…

ArrayTools
Desktop

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.…

AffyExpress
Desktop

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.

Eureka-DMA
Desktop

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.

EzArray
Web
Desktop

EzArray

Helps researchers for Affymetrix expression array data management and analysis.…

Helps researchers for Affymetrix expression array data management and analysis. EzArray organizes microarray data into projects that can be analyzed online with predefined or custom procedures.…

AMDA
Desktop

AMDA Automated Microarray Data Analysis

Provides scientists an easy and integrated system for the analysis of…

Provides scientists an easy and integrated system for the analysis of Affymetrix microarray experiments. AMDA covers all of steps, performing a full data analysis, including image analysis, quality…

ExonMiner
Web

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…

ArrayMining
Web

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.

R/maanova
Desktop

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…

TAC Software
Desktop

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…

Qlucore Omics…
Desktop

Qlucore Omics Explorer

Provides bioinformatics products to support the user with visual analysis of…

Provides bioinformatics products to support the user with visual analysis of measured data taking into account publicly available information such as gene ontologies, pathways and other system…

AMP
Web

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.

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

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)…

GeneSpring GX
Desktop

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.

GenomeStudio
Desktop

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…

Genedata…
Desktop

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.

INCLUSive
Web

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…

A A A
GAT
Web

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.…

IlluminaGUI
Desktop

IlluminaGUI

Enables the interested life scientist analyzing microarray experiments based on…

Enables the interested life scientist analyzing microarray experiments based on the increasingly used Illumina technology. IlluminaGUI is a graphical user interface implemented for analyzing…

YASMA
Desktop

YASMA Yet Another Statistical Microarray Analysis

Uses as an R library for the ANOVA analysis of replicated microarray…

Uses as an R library for the ANOVA analysis of replicated microarray experiments. YASMA is an add-on library for the R statistical package and can be used to analyse simple replicated experiments.…

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