About NetworkAnalyst

NetworkAnalyst has been developed as an easy-to-use and high-performance web-based program for biological network analysis and visualization. It also features several other unique statistics and visualization methods for omics data exploration. The long-term goal of the NetworkAnalyst project is to become a statistical and network-based systems biology platform for dissecting complex and high-dimensional omics datasets.

NetworkAnalyst publications

  • Xia J, Gill E, and Hancock REW (2015) "NetworkAnalyst for Statistical, Visual and Network-based Approaches for Meta-analysis of Expression Data" Nature Protocols 10, 823–844
  • Xia J, Benner MJ, and Hancock REW (2014) "NetworkAnalyst - integrative approaches for protein–protein interaction network analysis and visual exploration" Nucl. Acids Res. 42 (W1): W167-W174. (PPI data analysis and visualization)
  • Xia, J., Lyle, N.H., Mayer, M., Pena, O.M. and Hancock, R.E.W. (2013) “INVEX - a web-based tool for integrative visualization of expression data”. Bioinformatics 29 (24), 3232-3234 (gene expression data analysis)
  • Xia, J., Fjell, C.D., Mayer, M., Pena, O.M., Wishart, D.S. and Hancock, R.E.W. (2013) “INMEX - a web-based tool for integrative meta-analysis of expression data”. Nucleic Acids Research 41, W63-W70. (meta-analysis)

Implementations:

  • Statistcal Analysis: Majority of the statistical analyses are based on R (3.3.2) using R packages below:
    "limma", "vsn", "edgeR", "DESeq2", "lattice", "Cairo", "RankProd","igraph", "MCL", "stringr", "RColorBrewer", "data.table","compiler", "globaltest", "preprocessCore", "sva"
  • Web Platform: The web application has been developed based on JavaServer Faces (JSF) using libraries below: "PrimeFaces (v6.0)", "jQuery EasyUI", "Sigma.js", "CanvasXpress"
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