Software and Analysis Tools

Web based tools for comparative genomics analysis:

Gene tables:
Aggregatibacter actinomycetemcomitans 

Propionibacterium acnes and P. humerusii

Fusobacterium nucleatum

Haemophilus parasuis

Fusobacterium necrophorum

Tools for network inference (incomplete list - under construction):

networkBMA (Bayesian Model Averaging) - developed by Chris Fraley, Wm. Chad Young, Ka Yee Yeung, Adrian Raftery (with contributions from Kenneth Lo).  Relevant manuscript: "Integrating external biological knowledge in the construction of regulatory networks from time-series expression data". Lo K, Raftery AE, Dombek KM, Zhu J, Schadt EE, Bumgarner RE, Yeung KY.BMC Syst Biol. 2012 Aug 16;6:101.

Tools for clustering and classification:

iBMA - iterativeBMA - developed by Ka Yee Yeung, University of Washington, Seattle, WA, with contributions from Adrian Raftery and Ian Painter

© Roger Bumgarner 2016