Different methods have been proposed for analyzing differentially expressed (DE) genes in microarray data. Methods based on statistical tests that incorporate expression level variability are used more commonly than those based on fold change (FC). However, FC based results are…
limma
Desktop

limma Linear Models for Microarray Data

Provides an integrated solution for analysing data from gene expression…

Provides an integrated solution for analysing data from gene expression experiments. limma contains rich features for handling complex experimental designs and for information borrowing to overcome…

globaltest
Desktop

globaltest

Allows researchers to use prior information on groupings of genes and to…

Allows researchers to use prior information on groupings of genes and to specifically investigate groups of genes that interest them from a biological point of view. When researchers have many…

Babelomics
Desktop
Web

Babelomics

A web application for the functional analysis of gene expression and genomic…

A web application for the functional analysis of gene expression and genomic data. Babelomics offers user-friendly access to a full range of methods that cover: (i) primary data analysis, (ii) a…

maSigPro
Desktop

maSigPro

A package specifically suited for the analysis of time-course gene expression…

A package specifically suited for the analysis of time-course gene expression data, which was developed originally for microarrays and hence was limited in its application to count data. Updated…

DEMI
Desktop

DEMI Differential Expression from Multiple Indicators

A differential expression framework that capitalizes on the high number of…

A differential expression framework that capitalizes on the high number of concurrent measurements. It extends to various experimental designs and target categories (transcripts, genes, genomic…

MACAT
Desktop

MACAT MicroArray Chromosome Analysis Tool

This library contains functions to investigate links between differential gene…

This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes.

betr
Desktop

betr Bayesian Estimation of Temporal Regulation

A package to identify differentially expressed genes in microarray time-course…

A package to identify differentially expressed genes in microarray time-course data. BETR explicitly uses the time-dependent structure of the data, employing an empirical Bayes procedure to stabilize…

EMDomics
Desktop

EMDomics

Uses the Earth mover’s distance to measure the overall difference between the…

Uses the Earth mover’s distance to measure the overall difference between the distributions of a gene’s expression in two classes of samples and uses permutations to obtain q-values for each…

G T A T C G C T A
ImpulseDE
Desktop

ImpulseDE

Captures single impulse-like progression patterns in high throughput time…

Captures single impulse-like progression patterns in high throughput time series datasets. ImpulseDE can be applied on any kind of high throughput gene expression data. It reports differentially…

TTCA
Desktop

TTCA Transcript Time Course Analysis

Analyses sparse and heterogeneous time course data with high detection…

Analyses sparse and heterogeneous time course data with high detection sensitivity and transparency. TTCA is specifically designed for the analysis of perturbation responses. It combines different…

FCROS
Desktop

FCROS

A fold change ranks ordering statistics based method for detecting…

A fold change ranks ordering statistics based method for detecting differentially expressed genes.

gprege
Desktop

gprege

A package for ranking differentially expressed gene expression time courses…

A package for ranking differentially expressed gene expression time courses through Gaussian process regression. gprege fits two GPs with the an RBF (+ noise diagonal) kernel on each profile. One GP…

DGCA
Desktop

DGCA Differential Gene Correlation Analysis

An R package for systematically assessing the difference in gene-gene…

An R package for systematically assessing the difference in gene-gene regulatory relationships under different conditions. DGCA contains functions to filter, process, save, visualize, and interpret…

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…

st
Desktop

st Shrinkage t

A model-free shrinkage estimate of the variance vector across genes. Shrinkage…

A model-free shrinkage estimate of the variance vector across genes. Shrinkage t is derived in a quasi-empirical Bayes setting. The new rank score is fully automatic and requires no specification of…

FEM
Desktop

FEM Functional Epigenetic Modules

Identifies gene modules of coordinated differential methylation and…

Identifies gene modules of coordinated differential methylation and differential expression in the context of a human interactome. FEM is a functional supervised algorithm that could be applied to…

SVAPLS
Desktop

SVAPLS

Implements Partial Least Squares regression to extract the hidden signals of…

Implements Partial Least Squares regression to extract the hidden signals of sample-specific heterogeneity in the data and uses them to find the genes that are actually correlated with the phenotype…

UITagCreator
Desktop

UITagCreator

A process for the creation of library tags that increases accuracy in…

A process for the creation of library tags that increases accuracy in identification of the source tissue with little processing time overhead. UITagCreator also identifies the tissue of origin…

Edge
Desktop

Edge Extraction of Differential Gene Expression

An open source, point-and-click software program for the significance analysis…

An open source, point-and-click software program for the significance analysis of DNA microarray experiments. EDGE can perform both standard and time course differential expression analysis. The…

CellCODE
Desktop

CellCODE cell-type COmputational Differential Estimation

A multi-step statistical framework that uses latent variable analysis to…

A multi-step statistical framework that uses latent variable analysis to analyze differential expression from mixture samples. This approach is based on latent variable analysis and is…

DiscriminantCut
Desktop

DiscriminantCut

Explores the linear decision boundary family. DiscriminantCut is a machine…

Explores the linear decision boundary family. DiscriminantCut is a machine learning methodology for robust differential expression analysis, which can be an avenue to significantly advance research…

Plsgenomics
Desktop

Plsgenomics Partial least squares Analyses for Genomics

A statistical approach based on partial least squares regression to infer the…

A statistical approach based on partial least squares regression to infer the true TFAs from a combination of mRNA expression and DNA-protein binding measurements. Plsgenomics is also statistically…

MFSelector
Desktop

MFSelector Monotonic Feature Selector

A system, easy to use even with no pre-existing knowledge, to identify gene…

A system, easy to use even with no pre-existing knowledge, to identify gene sets with monotonic expression patterns in multi-stage as well as in time-series genomics matrices. The case studies on…

cDNA…
Desktop

cDNA Microarray Analysis

Assess the significance of gene effects in comparative experiments. cDNA…

Assess the significance of gene effects in comparative experiments. cDNA Microarray Analysis is based on a hierarchical model that incorporates several levels of variations. A version of empirical…

NUDGE
Desktop

NUDGE Normal Uniform Differential Gene Expression

Uses a simple univariate normal-uniform mixture model, in combination with new…

Uses a simple univariate normal-uniform mixture model, in combination with new normalization methods for spread as well as mean that extend the lowess normalization. NUDGE is a simple method to find…

G T A T C G C T A
cdc_RNASEQ
Desktop

cdc_RNASEQ

A differentially expressed (DE) gene selection algorithm, which controls the…

A differentially expressed (DE) gene selection algorithm, which controls the FDR based on predictive Bayesian estimates. The simulation studies empirically showed that the proposed confident…

waveTiling
Desktop

waveTiling

Implements a wavelet-based model for analyzing transcriptome data and extends…

Implements a wavelet-based model for analyzing transcriptome data and extends it towards more complex experimental designs. With waveTiling, the user is able to discover group-wise expressed regions,…

LimmaRP
Web

LimmaRP

Investigates and optimizes the performance of three statistical approaches by…

Investigates and optimizes the performance of three statistical approaches by using simulated and experimental data sets with varying numbers of missing values. LimmaRP uses three tools, including…

Bgmix
Desktop

Bgmix

Differences gene expression. BGmix uses a C++ routine to fit the chosen model…

Differences gene expression. BGmix uses a C++ routine to fit the chosen model via an Markov chain Monte Carlo (MCMC) algorithm. Files are written to a sub-directory in the working directory. The tool…

TWILIGHT
Desktop

TWILIGHT

Performs compatibly in detecting the shape of the local false discovery rate.…

Performs compatibly in detecting the shape of the local false discovery rate. TWILIGHT includes several functions for the statistical analysis of two-condition microarray data. TWILIGHT has a smaller…

multtest
Desktop

multtest

Non-parametric bootstrap and permutation resampling-based multiple testing…

Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise…

factDesign
Desktop

factDesign

A package that provides a set of tools for analyzing data from a factorial…

A package that provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions of…

LMGene
Desktop

LMGene

A package for analysis of microarray data using a linear model and glog data…

A package for analysis of microarray data using a linear model and glog data transformation. LMGene allows the identification of Differentially Expressed Genes in Gene Expression Arrays.

DEDS
Desktop

DEDS Differential Expression via Distance Summary

This library contains functions that calculate various statistics of…

This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics…

OCplus
Desktop

OCplus

Allows to characterize the operating characteristics of a microarray…

Allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. OCplus includes tools…

pickgene
Desktop

pickgene

Adaptive Gene Picking for Microarray Expression Data Analysis. Pickgene…

Adaptive Gene Picking for Microarray Expression Data Analysis. Pickgene provides functions to Analyze Microarray (Gene Expression) Data.

bridge
Desktop

bridge Bayesian Robust Inference for Differential Gene Expression

A package offering test for differentially expressed genes with microarray…

A package offering test for differentially expressed genes with microarray data. Bridge can be used with both cDNA microarrays or Affymetrix chip. It fits a robust Bayesian hierarchical model for…

lapmix
Desktop

lapmix

A package based on a Laplace mixture modelling of microarray experiments. A…

A package based on a Laplace mixture modelling of microarray experiments. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. The main purpose of…

plgem
Desktop

plgem

Models the variance-versus-mean dependence that exists in a variety of…

Models the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. PLGEM improves the detection of differentially expressed genes…

timecourse
Desktop

timecourse

Offers functions for data analysis and graphical displays for developmental…

Offers functions for data analysis and graphical displays for developmental microarray time course data.

HEM
Desktop

HEM

Heterogeneous error model for identification of differentially expressed genes…

Heterogeneous error model for identification of differentially expressed genes under multiple conditions.

LPE
Desktop

LPE

A library used to do significance analysis of microarray data with small number…

A library used to do significance analysis of microarray data with small number of replicates. LPE uses resampling based FDR adjustment, and gives less conservative results than traditional…

CellMix
Desktop

CellMix

Provides a comprehensive set of functionalities that together facilitate the…

Provides a comprehensive set of functionalities that together facilitate the exploration, assessment and deconvolution of gene expression data generated from heterogeneous biological samples. It…

ROAST
Desktop

ROAST

A statistically rigorous gene set test that allows for gene-wise correlation…

A statistically rigorous gene set test that allows for gene-wise correlation while being applicable to almost any experimental design. Instead of permutation, ROAST uses rotation, a Monte Carlo…

CTen
Web

CTen Cell Type enrichment

Determines if the observed gene regulation is the result of changes in the…

Determines if the observed gene regulation is the result of changes in the cellular make up of the sample. CTen can distinguish between active gene transcription and apparent gene expression…

CDF
Desktop

CDF Chip Definition Files

Encodes the physical design of the microarray and contain the sequence details…

Encodes the physical design of the microarray and contain the sequence details to link the oligonucleotide probes of the chip to the interrogated transcripts. CDFs is a set of custom for Affymetrix…

IBMT
Desktop

IBMT Intensity-Based Moderated T-statistic

A statistical testing procedure that further improves upon current methods by…

A statistical testing procedure that further improves upon current methods by incorporating the well-documented relationship between the absolute gene expression level and the variance of gene…

SAM
Desktop

SAM Significance Analysis of Microarrays

A statistical technique for finding significant genes in a set of microarray…

A statistical technique for finding significant genes in a set of microarray experiments.

GEDA
Web

GEDA Gene Expression Data Analyzer

Provides the academic community with free and reliable web tools for…

Provides the academic community with free and reliable web tools for Bioinformatics and Genome research. GEDA provides a gene expression data analysis tool. The GEDA tool calculates the averages of…

Curators for Differential expression detection

  • Marc Delord's avatar image
    Marc Delord
    University Paris Diderot, Paris,…
Information

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