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…
Desktop app
Web app
Babelomics Babelomics

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…

Desktop app
Linear Models for… Linear Models for Microarray Data

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…

Desktop app
TWILIGHT TWILIGHT

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…

Desktop app
Transcript Time… Transcript Time Course Analysis

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…

Desktop app
EMDomics EMDomics

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…

Desktop app
Differential Gene… Differential Gene Correlation Analysis

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…

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
G T A T C G C T A ImpulseDE ImpulseDE

ImpulseDE

An R package suited to capture single impulse-like progression patterns in high…

An R package suited to capture 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…

Desktop app
Partial least squares… Partial least squares Analyses for Genomics

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…

Desktop app
Shrinkage t Shrinkage t

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…

Desktop app
cDNA Microarray… cDNA Microarray Analysis

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…

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Chip Definition Files Chip Definition Files

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…

Desktop app
DiscriminantCut DiscriminantCut

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…

Desktop app
Intensity-Based… Intensity-Based Moderated T-statistic

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…

Web app
LimmaRP LimmaRP

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…

Desktop app
Extraction of… Extraction of Differential Gene Expression

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…

Desktop app
Monotonic Feature… Monotonic Feature Selector

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…

Desktop app
G T A T C G C T A cdc_RNASEQ cdc_RNASEQ

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…

Desktop app
cell-type… cell-type COmputational Differential Estimation

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…

Desktop app
CellMix CellMix

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…

Desktop app
ROAST ROAST

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…

Desktop app
Differential… Differential Expression from Multiple Indicators

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…

Desktop app
FCROS FCROS

FCROS

A fold change ranks ordering statistics based method for detecting…

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

Desktop app
globaltest globaltest

globaltest

A package that tests groups of covariates (or features) for association with a…

A package that tests groups of covariates (or features) for association with a response variable. Globaltest implements the test with diagnostic plots and multiple testing utilities, along with…

Desktop app
multtest multtest

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…

Desktop app
factDesign factDesign

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…

Desktop app
gprege gprege

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…

Desktop app
LMGene LMGene

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.

Desktop app
waveTiling waveTiling

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,…

Desktop app
Differential… Differential Expression via Distance Summary

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…

Desktop app
OCplus OCplus

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…

Desktop app
pickgene pickgene

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.

Desktop app
Bayesian Estimation… Bayesian Estimation of Temporal Regulation

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…

Desktop app
Bayesian Robust… Bayesian Robust Inference for Differential Gene…

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…

Desktop app
lapmix lapmix

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…

Desktop app
maSigPro maSigPro

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…

Desktop app
MicroArray Chromosome… MicroArray Chromosome Analysis Tool

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.

Desktop app
plgem plgem

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…

Desktop app
timecourse timecourse

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.

Desktop app
HEM HEM

HEM

Heterogeneous error model for identification of differentially expressed genes…

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

Desktop app
LPE LPE

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…

Desktop app
Significance Analysis… Significance Analysis of Microarrays

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.

Curators for Differential expression detection

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