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Wikiomics:Pathway analysis: Difference between revisions
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* [http://www.bioinformatics.ubc.ca/ermineJ/ ErmineJ] "ErmineJ performs analyses of gene sets in expression microarray data. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists with little or no informatics background." | * [http://www.bioinformatics.ubc.ca/ermineJ/ ErmineJ] "ErmineJ performs analyses of gene sets in expression microarray data. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists with little or no informatics background." | ||
* [http://www.bioconductor.org/packages/release/bioc/html/gage.html GAGE] is applicable independent of sample sizes, experimental design, assay platforms, and other types of heterogeneity ( [http://www.biomedcentral.com/1471-2105/10/161 paper]). This Biocondutor package also provides functions and data for pathway, GO and gene set analysis in general. | * [http://www.bioconductor.org/packages/release/bioc/html/gage.html GAGE] is applicable independent of sample sizes, experimental design, assay platforms, and other types of heterogeneity ([http://www.biomedcentral.com/1471-2105/10/161 paper]). This Biocondutor package also provides functions and data for pathway, GO and gene set analysis in general. | ||
=Other tools to check= | =Other tools to check= | ||
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* [http://www.cytoscape.org/ Cytoscape] leader in the field | * [http://www.cytoscape.org/ Cytoscape] leader in the field | ||
* [http://www.ondex.org/ ONDEX] [http://bioinformatics.oxfordjournals.org/cgi/content/full/22/11/1383 HTML] "enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques" | * [http://www.ondex.org/ ONDEX] [http://bioinformatics.oxfordjournals.org/cgi/content/full/22/11/1383 HTML] "enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques" | ||
* [http://bioconductor.org/packages/2.12/bioc/html/pathview.html Pathview] | * [http://bioconductor.org/packages/2.12/bioc/html/pathview.html Pathview] R/Bioconductor tool for pathway based data integration and visualization, easy to integrate in pathway analysis workflows. [http://pathview.r-forge.r-project.org/ R-Forge]has an overview with some nice example plots. The work has been published in [http://bioinformatics.oxfordjournals.org/content/early/2013/06/11/bioinformatics.btt285.full Bioinformatics]. | ||
=Protein interactions= | =Protein interactions= | ||
