![]() ![]() Yoneda M, Yoshikane T, Motooka N et al (2005) Stimulation of growth of Porphyromonas gingivalis by cell extracts from Tannerella forsythia. The Cytoscape Consortium (2019) Cytoscape user manual. Layeghifard M, Hwang DM, Guttman DS (2018) Constructing and analyzing microbiome networks in R. Unfortunately, a current version of the rgexf package does not support real-time network visualization and exploration. Lahti L, Salojärvi J, Salonen A, Scheffer M, de Vos WM (2014) Tipping elements in the human intestinal ecosystem. Gephi is a great network visualization tool that allows real-time network visualization and exploration, including network data spatializing, filtering, calculation of network properties, and clustering. Tipton L, Müller CL, Kurtz ZD, Huang L, Kleerup E, Morris A et al (2018) Fungi stabilize connectivity in the lung and skin microbial ecosystems. Schwager E, Weingart G, Bielski C, Huttenhower C (2014) CCREPE: compositionality corrected by permutation and renormalization But I really want to put them in a graph. PLoS Comput Biol 11:1–25įriedman J, Alm EJ (2012) Inferring correlation networks from genomic survey data. So I could do a line graph of each and plot the models on a line of similar to most different. ![]() ![]() Kurtz ZD, Müller CL, Miraldi ER, Littlman DR, Blaser MJ, Bonneau RA (2015) Sparse and compositionally robust inference of microbial ecological networks. Cytoscape: a software environment for integrated models of biomolecular inter-action networks. Steele JA, Countway PD, Xia L, Vigil PD, Beman JM, Beman M et al (2011) Marine bacterial, archaeal and protistan association networks reveal ecological linkages. Gephi: An Open Source Software for Exploring and Manipulating Networks Mathieu Bastian and Sebastien Heymann Gephi, WebAtlas. Sullivan MJP, Talbot J, Lewis SL, Phillips OL, Qie L, Begne SK et al (2017) Diversity and carbon storage across the tropical forest biome. Nature 515:505–511īanerjee S, Walder F, Büchi L, Meyer M, Held AY, Gattinger A et al (2019) Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. Bardgett RD, Van Der Putten WH (2014) Belowground biodiversity and ecosystem functioning. ![]()
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