Functional enrichment analysis software tools | Gene expression

Functional enrichment analysis can help reveal biological insights from high-throughput omics data. It has become indispensable in today's biological studies. There are three well-established and complementary methods for enrichment analysis, including Over-Representation…

Functional enrichment analysis steps

Most recent bioinformatics tools

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HEAT
Web

HEAT H-InvDB Enrichment Analysis Tool

Identifies automatically features specific to a given human gene set. HEAT is a…

Identifies automatically features specific to a given human gene set. HEAT is a data mining tool that searches H-InvDB annotations that are significantly enriched in a user-defined gene set, as…

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TPEA
Desktop

TPEA Topology-based Pathway Enrichment Analysis

Performs pathway enrichment analysis. TPEA evaluates the importance of nodes…

Performs pathway enrichment analysis. TPEA evaluates the importance of nodes based on their global upstream/downstream positions and the degrees in pathways. It was tested on six gene expression…

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GeneTopics
Algorithm

GeneTopics

Ccombines ideas from gene set enrichment with topic model inference. GeneTopics…

Ccombines ideas from gene set enrichment with topic model inference. GeneTopics is able to quickly and comprehensively identify topics in the literature that a biologist should consider when…

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paraGSEA
Desktop

paraGSEA

Accelerates querying of large-scale transcription profiles all-pairs comparison…

Accelerates querying of large-scale transcription profiles all-pairs comparison and global clustering analysis on transcriptomic datasets. paraGSEA is based on a scalable parallel algorithm. It is…

Most popular analytical software

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Enrichr
Web

Enrichr

An integrative web-based and mobile software application that includes new…

An integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to…

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g:Profiler
Web

g:Profiler

Provides tool to perform functional enrichment analysis and mine additional…

Provides tool to perform functional enrichment analysis and mine additional information. g:Profiler is a web server that allows to characterize and manipulate gene lists of high-throughput genomics.…

STEM
Desktop

STEM Short Time-series Expression Miner

A software program specifically designed for the analysis of short time series…

A software program specifically designed for the analysis of short time series microarray gene expression data. STEM implements unique methods to cluster, compare, and visualize such data. STEM also…

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DESeq
Desktop

DESeq

A method for differential analysis of RNA-sequencing count data, using…

A method for differential analysis of RNA-sequencing count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a…

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