External Tool List
Links to other useful tools for the scientific community.- agriGO
- ArrayTrack/Goffa - An integrated environment for microarray data management, analysis and interpretation.
- BiNGO - A Biological Network Gene Ontology Enrichment tool
- bioPIXIE - Discovery of biological networks from diverse functional genomic data
- Blast2GO - functional annotation of (novel) sequences and the analysis of annotation data.
- CLASSIFI - a microarray gene cluster classification tool
- CLENCH - calculate cluster enrichment using the Gene Ontology
- CLueGO for Cytoscape - visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network
- Cytoscape - Network Data Integration, Analysis, and Visualization
- DryGin - Data Repository of Yeast Genetic Interactions
- EASE - Expression Analysis Systematic Explorer
- EGAN - Exploratory Gene Association Networks
- eGOn/GENETOOLS - interpreting and statistical analysis of genomic data or other interesting gene sets using Gene Ontology
- ermineJ - Gene Ontology analysis for high-throughput data
- FatiGO
- FatiScan - detects blocks of genes functionally related
- FunSpec - gene enrichment
- FunAssociate 2.0 - The Gene Set Functionator
- FunCluster - functional analysis of gene expression data obtained from cDNA microarray experiments
- FunNet - tool for analyzing gene co-expression networks built from microarray expression data
- GAzer - identifies significantly changed gene sets scored by z-statistics and p-vales from z-test or permutation test
- Gene Class Expression
- GFINDer - Genome Function INtegrated Discoverer - search for biological features (annotations) that frequently co-occur in a set of genes
- GENECODIS - search for biological features (annotations) that frequently co-occur in a set of genes and rank them by statistical significance
- GeneMerge - provides statistical rank scores for over-representation of particular functions or categories in a genomic dataset
- GeneTrail - Over-Representation Analysis and Gene Set Enrichment Analysis
- GenMAPP - Gene Map Annotator and Pathway Profiler
- GO-2D - finds 2-dimensional functional modules based on combined GO categories
- GOALIE - GO Algorithmic Logic for Information Extraction
- GObar - GENE LIST ANALYSIS using GENE ONTOLOGY
- GO-Cluster - visual interpretation of microarray data
- GOdist for MATLAB - analyzes Affymetrix microarray expression data implementing Kolmogorov-Smirnov (KS) continuous statistics approach
- GOEAST - Gene Ontology Enrichment Analysis Software Toolkit
- GOEx - leverages the gene ontology (GO) to aid in the interpretation of proteomic data
- GOHyperGALL - R program to test a sample population of genes for over-representation of GO terms
- GOLEM - an interactive graph-based gene-ontology navigation and analysis tool
- GOlorize for Cytoscape - uses Gene Ontology (GO) categories or other additional class information to direct the network graph layout process and to emphasize the biological function of the nodes
- GO-Mapper - Functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms
- GoMiner - a tool for biological interpretation of 'omic' data
- g:profiler - a web-based toolset for functional profiling of gene lists from large-scale experiments
- GORILLA - Gene Ontology enRIchment anaLysis and visuaLizAtion tool
- G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools
- GOSim - R package - Computation of functional similarities between GO terms and gene products
- GO SlimMapper at SGD - maps annotations of a group of genes to more general terms and/or bins them into broad categories
- GOstat - Find statistically overrepresented GO terms within a group of genes
- GOsurfer - uses Gene Ontology (GO) information to analyze gene sets obtained from genome-wide computations or microarray analyses
- GO TermFinder at SGD - searches for significant shared GO terms, or parents of those GO terms
- GOToolBox - a series of programs allowing the functional investigation of groups of genes, based on the Gene Ontology resource
- GraphWeb - public web server for graph-based analysis of biological networks
- GREAT - Genomic Regions Enrichment of Annotations Tool
- GSEA - Gene Set Enrichment Analysis
- JProGO - Gene Ontology-based interpretation of prokaryotic microarray data
- L2L - A simple tool for discovering the hidden biological significance in microarray expression data
- Marmite - My Accurate Resource for MIning TExt
- MarmiteScan - a threshold free method (FatiScan) that extracts blocks of related genes from an ordered list of genes
- MetaGP - Web service for significance test of differentially-expressed Meta Genes
- MeV - MultiExperiment Viewer (analysis, visualization and data-mining of large-scale genomic data)
- Onto-Compare - software package for comparing the functional bias of different commercially available or custom microarrays
- Onto-Design - database to assist the designers of custom microarrays
- Onto-Express - software package for the rapid functional profiling of a set of genes
- Onto-Miner - provides a single and convenient interface that allows the user to interrogate the databases regarding annotations of known genes
- Onto-Translate - software package designed to translate a list of genes in one format into another
- Ontologizer - A Tool for Statistical Analysis and Visualization of High-Throughput Biological Data Using Gene Ontology
- PageMan - a tool to get a quick overview of multiparallel experiments
- PaLS - filters gene/clone/protein identifiers based on those that meet certain criteria related to their references to articles in PubMed, Gene Ontology terms and KEGG and Reactome pathways
- POSOC - R package for Probabilistic Categorical Data analysis
- ProbCD - Probabilistic Categorical Data analysis
- ProfCom - tool for the interpretation of genes that were identified to be functionally linked by experiment
- SOURCE - pools publicly available data commonly sought after for any clone, GenBank accession number, or gene
- STEM - Short Time-series Expression Miner
- THEA - Ontology driven analysis of microarray data
- TopGO - Enrichment analysis for Gene Ontology
- T-profiler - Scoring the activity of pre-defined groups of genes using gene expression data
- visANT - an integrative framework for networks in systems biology
- WebBayGO - Bayesian analysis of ontology term enrichment in microarray data
- WebGestalt - WEB-based GEne SeT AnaLysis Toolkit
- WEGO - Web Gene Ontology Annotation Plotting
