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AMEN (Annotation, Mapping, Expression and Network) is a stand-alone, unified suite of tools to manage, explore and combine biological multifaceted high-throughput data such as annotation, chromosomal location, expression and interaction data.
Suite of community detection algorithms based on Modularity
- MixtureModel_v1r1: overlapping community algorithm [3], which includes novel partition density and fuzzy modularity metrics.
- OpenMP versions of algorithms in [1] are available to download.
- Main suite containing three community detection algorithms based on the Modularity measure containing: Geodesic and Random Walk edge Betweenness [1] and Spectral Modularity [2].
Collaborator: Theologos Kotsos.
[1] M. Newman & M. Girvan, Physical Review, E 69 (026113), 2004.
[2] M. Newman, Physical...
... suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline." Source Code for Biology and Medicine, 2014 9:30]
HeatmapGenerator source code is available at: https://github.com/Bohdan-Khomtchouk/HeatmapGenerator
Bohdan Khomtchouk wishes to acknowledge the support of the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program.
HeatmapGenerator is released under the GNU GPL.
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