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We have implemented an R package called MODA (Module Differential Analysis) for gene co-expression network differential analysis. Based on transcriptomic data, MODA can be used to estimate and construct condition-specific gene co-expression networks, and identify differentially expressed subnetworks as conserved or condition specific modules which are potentially associated with relevant biological processes. The usefulness of the method is also demonstrated by synthetic data as well as Daphnia magna gene expression data under different environmental stresses.}, URL = {http://biorxiv.org/content/early/2016/06/03/053496}, eprint = {http://biorxiv.org/content/early/2016/06/03/053496.full.pdf}, journal = {bioRxiv} } @article{blondel2008fast, title={Fast unfolding of communities in large networks}, author={Blondel, Vincent D and Guillaume, Jean-Loup and Lambiotte, Renaud and Lefebvre, Etienne}, journal={Journal of statistical mechanics: theory and experiment}, volume={2008}, number={10}, pages={P10008}, year={2008}, publisher={IOP Publishing} } @inproceedings{white2005spectral, title={A Spectral Clustering Approach To Finding Communities in Graph.}, author={White, Scott and Smyth, Padhraic}, booktitle={SDM}, volume={5}, pages={76--84}, year={2005}, organization={SIAM} } @Misc{li2016amountain, title={AMOUNTAIN: Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach}, author={Li, Dong and Pan, Zhisong and Hu, Gongyu and He, Shan}, url = {http://bioconductor.org/packages/AMOUNTAIN}, version = {1.0.0}, year={2016} }