Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Unclassified tools | Gene expression microarray data analysis

Onto-Design
Web

Onto-Design

Allows the user to select genes that represent given functional categories.…

Allows the user to select genes that represent given functional categories. Onto-Design permits to create customized array representing some chosen biological processes. It provides the means to…

SPELL
Web

SPELL Serial Pattern of Expression Levels Locator

Enables biology researchers to explore the entirety of very large microarray…

Enables biology researchers to explore the entirety of very large microarray compendia in a biologically meaningful manner. SPELL is a scalable, context-specific search methodology implemented in an…

massiR
Desktop

massiR

Provides a method for researchers to predict the sex of samples in microarray…

Provides a method for researchers to predict the sex of samples in microarray datasets.

CIBERSORT
Web
Myriads
Desktop

Myriads

Provides methods for computing different p-value based correction methods.…

Provides methods for computing different p-value based correction methods. Myriads incorporates a simulator for two sample t-tests and Cochran-Armitage case-control tests. The simulator can be used…

quantroSim
Desktop

quantroSim

An R-package to simulate gene expression and DNA methylation data. The…

An R-package to simulate gene expression and DNA methylation data. The R-package quantroSim is the supporting data simulation package for the quantro R/Bioconductor package which can be used to…

TREBAX
Desktop

TREBAX

Provides a prediction method for transcription units (TU prediction) in the…

Provides a prediction method for transcription units (TU prediction) in the bacterial whole genome. TREBAX uses integrated analysis of microarray and DNA sequence data to identify unknown TUs and…

irMF
Desktop

irMF

Assists users in research on microarrays, proteomics and metabolomics. irMF…

Assists users in research on microarrays, proteomics and metabolomics. irMF uses non-negative matrix factorization to create groups of genes and sets of predictors. It uses non-negative matrix…

MGFM
Web
Desktop

MGFM Marker Gene Finder in Microarray data

Predicts tissue/cell type marker genes using microarray gene expression data.…

Predicts tissue/cell type marker genes using microarray gene expression data. The main advantages of MGFM are i) a short running time of some seconds per analysis. This is achieved by sorting the…

GeneRank
Algorithm

GeneRank

Combines connectivity and expression data to produce a robust summary of an…

Combines connectivity and expression data to produce a robust summary of an experiment. GeneRank is based on the PageRank algorithm and increase its capabilities to rank genes in microarray…

spkTools
Desktop

spkTools

Enables cross-platform comparisons, and proposes a comprehensive procedure for…

Enables cross-platform comparisons, and proposes a comprehensive procedure for assessments based on spike-in experiments. spkTools is implemented as a user friendly Bioconductor package. It contains…

qpgraph
Desktop

qpgraph

Estimates gene and eQTL networks from high-throughput expression and genotyping…

Estimates gene and eQTL networks from high-throughput expression and genotyping assays. qpgraph is based in the so-called q-order limited partial correlation graphs, qp-graphs, which is specifically…

CAFE
Desktop

CAFE

Follows the expression based karyotyping workflow (e-karyotyping) and greatly…

Follows the expression based karyotyping workflow (e-karyotyping) and greatly simplifies and speeds up the detection analysis of chromosomal aberrations from expression DNA microarrays.

MaLTE
Desktop

MaLTE Machine Learning of Transcript Expression

An alternative approach to gene expression estimation that uses a machine…

An alternative approach to gene expression estimation that uses a machine learning approach. MaLTE relies on a gold standard (such as RNA-Seq) to infer gene expression models that make better use of…

TFInfer
Desktop

TFInfer

Evaluates transcription factor (TF) activities according to gene-expression…

Evaluates transcription factor (TF) activities according to gene-expression data combined with architectural information about the regulatory network. TFInfer allows users to visualize TF activity, a…

DetectiV
Desktop

DetectiV

Offers powerful yet simple visualization, normalization and significance…

Offers powerful yet simple visualization, normalization and significance testing tools. DetectiV uses simple and well established visualization and statistical techniques to analyze data from…

SPEC
Desktop

SPEC Subset Prediction from Enrichment Correlation

Supports blood genomics studies with general applicability to basic and…

Supports blood genomics studies with general applicability to basic and translational research. SPEC predicts the cellular source of predictive gene expression signatures using transcriptional…

eXPatGen
Web

eXPatGen

A simulator of gene expression patterns in order to evaluate different analysis…

A simulator of gene expression patterns in order to evaluate different analysis methods, such as clustering and principle component analysis (PCA).

AtMIAMExpress
Desktop

AtMIAMExpress

Uses as submission tool for Microarray experiments. AtMIAMExpress is an…

Uses as submission tool for Microarray experiments. AtMIAMExpress is an open-source Web-based software application for the submission of Arabidopsis-based microarray data to ArrayExpress. It was…

infino
Desktop

infino

Encodes the immune cell lineage relationships and produces rich confidence…

Encodes the immune cell lineage relationships and produces rich confidence scores at all levels of the hierarchy of immune cell types. Infino is a Bayesian regression mixture deconvolution method…

immunoStates
Desktop

immunoStates

Provides a basis matrix. immunoStates is constructed by extracting over 6200…

Provides a basis matrix. immunoStates is constructed by extracting over 6200 microarray samples from 166 public gene expression datasets with the aims of decreasing biological and technical biases,…

Oncopression
Web

Oncopression

Provides graphical comparison results between normal and cancer with student…

Provides graphical comparison results between normal and cancer with student t-test statistics. Oncopression is focused on microarray-based gene expression profiles for normal and cancer. This web…

pcaMethods
Desktop

pcaMethods principal component analysisMethods

A compliant library for computing principal component analysis on incomplete…

A compliant library for computing principal component analysis on incomplete data sets. pcaMethods combines an expectation maximization approach with a probabilistic model. It also offers methods for…

MASQOT-GUI
Desktop

MASQOT-GUI

An open-source, platform-independent software pipeline for two-channel…

An open-source, platform-independent software pipeline for two-channel microarray spot quality control. MASQOT-GUI hosts a set of independent applications for gridding, segmentation, quantification,…

UNDO
Desktop

UNDO UNsupervised DecOnvolution

An R package that can be used to automatically detect cell-specific marker…

An R package that can be used to automatically detect cell-specific marker genes (MGs) located on the scatter radii of mixed gene expressions, estimate cellular proportions in each sample and…

madsim
Desktop

madsim MicroArray Data Simulation Model

Allows to generate two conditions biological synthetic microarray dataset with…

Allows to generate two conditions biological synthetic microarray dataset with known characteristics. madsim is a flexible microarray data simulation model where user provides a subset of parameters.…

GiGA
Desktop

GiGA Graph-based iterative Group Analysis

A fast and flexible delimitation of the most interesting areas in a microarray…

A fast and flexible delimitation of the most interesting areas in a microarray experiment. GiGA identifies all relevant physiological processes, puts them into context, summarizes them in an…

SDRF2GRAPH
Web

SDRF2GRAPH

Permits graphical representation of a wide range of Sample and Data…

Permits graphical representation of a wide range of Sample and Data Relationship Format (SDRF) files. SDRF2GRAPH assists researchers to describe and exchange information about experiments. It…

G T A T C G C T A
TReNA
Desktop

TReNA

Permits to reconstruct transcriptional regulatory networks. TReNA uses gene…

Permits to reconstruct transcriptional regulatory networks. TReNA uses gene expression, priors, machine learning to process. It is particularly useful in species for which genome-wide transcription…

DeMix
Desktop

DeMix

A statistical method for deconvolving mixed cancer transcriptomes which…

A statistical method for deconvolving mixed cancer transcriptomes which addresses the aforementioned issues in array-based expression data. DeMix can be applied to ongoing biomarker-based clinical…

MiningABs
Desktop

MiningABs

A meta-analysis method able to efficiently identify associated biomarkers (ABs)…

A meta-analysis method able to efficiently identify associated biomarkers (ABs) from different independently performed array-based datasets. MiningABs quantifies the similarity between paired probe…

phylochipanalys…
Desktop

phylochipanalyser

A Windows-program for the analysis of experiments with hierarchical probe-sets.…

A Windows-program for the analysis of experiments with hierarchical probe-sets. PhylochipAnalyzer operates in two modes: first, the hierarchy of probes is defined interactively; second, the intensity…

GEMS
Desktop

GEMS Gene Expression Model Selector

Provides gene expression model analyzer. GEMS is a system for automated…

Provides gene expression model analyzer. GEMS is a system for automated development and evaluation of cancer diagnostic models and biomarker discovery from microarray gene expression data. It…

KegArray
Desktop

KegArray

Provides an environment for analyzing both transcriptome data (gene expression…

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…

KNNimpute
Desktop

KNNimpute

Estimates missing values for microarray data. KNNimpute provides accurate…

Estimates missing values for microarray data. KNNimpute provides accurate estimation for missing values in genes that belong to small tight expression clusters.

TM4 Microarray…
Desktop

TM4 Microarray Software Suite

Allows users to collect, manage, and effectively analyze data from microarray…

Allows users to collect, manage, and effectively analyze data from microarray experiments. TM4 Microarray Software Suite is composed of a set of four tools: Madam, Spotfinder, Midas and MeV. It…

MVIAeval
Web

MVIAeval

Allows researchers to easily conduct a comprehensive and objective performance…

Allows researchers to easily conduct a comprehensive and objective performance evaluation of their newly developed missing value imputation algorithm for microarray data or any data which can be…

ALLENMINER
Desktop

ALLENMINER

Enables a range of flexible query mechanisms for Allen Brain Atlas (ABA).…

Enables a range of flexible query mechanisms for Allen Brain Atlas (ABA). ALLENMINER allows users to define custom regions of interest, search for genes that are graded or patterned in regions of…

MADGene
Web

MADGene

Allows the user to convert id lists in order to unify heterogeneous gene sets.…

Allows the user to convert id lists in order to unify heterogeneous gene sets. MADGene is a software environment comprising a web-based database and a java application. This database creates bridges…

MAGE-ML
Desktop

MAGE-ML Microarray Gene Expression Markup Language

Retrieves data from different microarray databases using MAGE-ML and for…

Retrieves data from different microarray databases using MAGE-ML and for combining microarray data with breast cancer image analysis and clinical data for correlation studies. MAGE-ML provides the…

PositionMatcher
Desktop

PositionMatcher

Allows annotation of massively parallel sequencing (MPS) read, microarray…

Allows annotation of massively parallel sequencing (MPS) read, microarray probes or any tag-based technologies to measure mRNA abundance. PositionMatcher provides tags with rich annotation…

Sample Sizes
Web

Sample Sizes

A tool to compute the number of samples needed to detect expression changes for…

A tool to compute the number of samples needed to detect expression changes for a microarray experiment.

MADAM
Desktop

MADAM MicroArray DAta Manager

Guides users through the microarray process from RNA procurement to data…

Guides users through the microarray process from RNA procurement to data analysis, offering intelligent forms to simplify the tracking of experimental parameters and results.

BCLUST
Desktop

BCLUST

Allows users to check genes clusters’ trustworthiness. BCLUST uses a parametric…

Allows users to check genes clusters’ trustworthiness. BCLUST uses a parametric bootstrap resampling approach to include information relative to variations in gene expression levels. It permits to…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.