CytoSaddleSum 1.5 – Functional Enrichment Analysis plugin for Cytoscape

CytoSaddleSum 1.5

:: DESCRIPTION

CytoSaddleSum provides Cytoscape users with access to the functionality of SaddleSum, a functional enrichment tool based on sum-of-weight scores.

::DEVELOPER

Yi-Kuo Yu

:: SCREENSHOTS

:: REQUIREMENTS

Linux/ Windows/ MacOsX
Java
Cytoscape

:: DOWNLOAD

CytoSaddleSum

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Mar 15;28(6):893-4. doi: 10.1093/bioinformatics/bts041. Epub 2012 Feb 15.
CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores.
Stojmirovic A1, Bliskovsky A, Yu YK.

FunRich 3.1.4 – Functional Enrichment analysis tool

FunRich 3.1.4

:: DESCRIPTION

FunRich is a stand-alone software tool used mainly for functional enrichment and interaction network analysis of genes and proteins.

::DEVELOPER

FunRich team

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

FunRich

:: MORE INFORMATION

Citation

FunRich: An open access standalone functional enrichment and interaction network analysis tool.
Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CY, Williamson NA, Mouradov D, Sieber OM, Simpson RJ, Salim A, Bacic A, Hill AF, Stroud DA, Ryan MT, Agbinya JI, Mariadason JM, Burgess AW, Mathivanan S.
Proteomics. 2015 Aug;15(15):2597-601. doi: 10.1002/pmic.201400515

Enrichment Map 3.2.1 – Cytoscape plugin for Functional Enrichment Visualization

Enrichment Map 3.2.1

:: DESCRIPTION

EnrichmentMap is a Cytoscape plugin for functional enrichment visualization. Enrichment results have to be generated outside Enrichment Map, using any of the available methods. Gene-sets, such as pathways and Gene Ontology terms, are organized into a network (i.e. the “enrichment map”). In this way, mutually overlapping gene-sets cluster together, making interpretation easier. Enrichment Map also enables the comparison of two different enrichment results in the same map.

::DEVELOPER

Bader Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java
Cytoscap

:: DOWNLOAD

EnrichmentMap

:: MORE INFORMATION

Citation

Merico D, Isserlin R, Stueker O, Emili A, Bader GD
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
PLoS One. 2010 Nov 15;5(11):e13984