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Differential co-expression analysis software tools | Gene expression data analysis

n the transcriptome analysis domain, differential co-expression analysis (DCEA) is emerging as a unique complement to traditional differential expression analysis. Rather than calculating expression level changes of individual genes, DCEA…
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cocor
Web
Desktop

cocor

Provides a wide range of tests for comparisons of independent and dependent…

Provides a wide range of tests for comparisons of independent and dependent correlations with either overlapping or nonoverlapping variables. cocor offers two convenient graphical user interfaces…

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SpeCond
Desktop

SpeCond Specific Condition

Detects condition-specificity from a dataset of gene expression measurements.…

Detects condition-specificity from a dataset of gene expression measurements. SpeCond is based on a normal mixture model to the expression profile of each gene, and identifies outlier conditions. It…

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BicOverlapper
Desktop

BicOverlapper

Allows to visualize complex gene expression analysis results coming from…

Allows to visualize complex gene expression analysis results coming from biclustering algorithms. BicOverlapper visualizes the most relevant aspects of the analysis, including expression data,…

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SegCorr
Desktop

SegCorr

Performs correlation matrix segmentation and applies a test procedure that…

Performs correlation matrix segmentation and applies a test procedure that permits to detect highly correlated regions in gene expression. SegCorr is a statistical procedure build for the…

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ISOexpresso
Dataset

ISOexpresso

Facilitates expression-based isoform-level analysis of large-scale TCGA (The…

Facilitates expression-based isoform-level analysis of large-scale TCGA (The Cancer Genome Atlas) multi-cancer RNA-seq data. ISOexpresso is a database which provides information regarding isoform…

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CellMapper
Desktop

CellMapper

Infers cell type-specific expression based on co-expression similarity with…

Infers cell type-specific expression based on co-expression similarity with known cell type marker genes. CellMapper is an R package that can make accurate predictions using publicly available…

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CSD
Desktop

CSD Conserved, Specific, Differentiated

Allows users to study co-expression genes variation. CSD classifies gene pairs…

Allows users to study co-expression genes variation. CSD classifies gene pairs thanks to mathematically defined scores to build a unified differential co-expression network from experimental data.…

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iDEP
Web
Desktop

iDEP Integrated Differential Expression and Pathway analysis

Analyzes gene expression data from DNA microarray or RNA-Seq. iDEP integrates…

Analyzes gene expression data from DNA microarray or RNA-Seq. iDEP integrates many commonly-used R/Bioconductor packages with comprehensive annotation databases. Normalized expression and RNA-Seq…

BCIP
Dataset

BCIP Breast Cancer Integrative Platform

Maintains multi-omics data selected with strict quality control and processed…

Maintains multi-omics data selected with strict quality control and processed with uniform normalization methods. BCIP is a database that provides a user-friendly interface integrating comprehensive…

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DiffCorr
Desktop

DiffCorr

A simple method for identifying pattern changes between 2 experimental…

A simple method for identifying pattern changes between 2 experimental conditions in correlation networks, which builds on a commonly used association measure, such as Pearson's correlation…

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Biotmle
Desktop

Biotmle

Computes the causal target parameter defined as the difference between the…

Computes the causal target parameter defined as the difference between the biomarker expression values under treatment and those same values under no treatment. Biotmle is an R package that…

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fCI
Desktop

fCI f-divergence Cutoff Index

Finds differentially expressed genes (DEGs) in the transcriptomic &…

Finds differentially expressed genes (DEGs) in the transcriptomic & proteomic data. fCI is a package that can be used to analysis transcriptomics and proteomics. It also identifies DEGs by…

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CorSig
Desktop

CorSig

A method for statistical inference of correlation significance. CorSig is based…

A method for statistical inference of correlation significance. CorSig is based on a biology-informed null hypothesis, i.e., testing whether the true PCC (ρ) between two variables is statistically…

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DCGL
Desktop

DCGL

Implements valuable differential co-expression analysis and differential…

Implements valuable differential co-expression analysis and differential regulation analysis methodologies. DCGL has universal applicability and is suitable for both microarray data and RNA-seq data.…

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