Genevera Allen
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Major Software Packages:

  • TCGA2STAT

    • Software to automatically download and process TCGA data into a format ready for integrated statistical analyses in R.

    • Online manual.

    • Authors: Ying-Wooi Wan, Genevera I. Allen, Zhandong Liu.

    • Citation: Y.W. Wan, G.I. Allen, and Z. Liu, "TCGA2STAT: Simple TCGA Data Access for Integrated Statistical Analysis in R", (To Appear) Bioinformatics 2015. [pdf]




  • MoNet: Markov Network Toolbox for Functional Connectivity (alpha-version).

    • Software for estimating functional brain connectivity networks (Markov Networks) from resting-state fMRI data and conducting population inference for assocaitions with network differences.

    • Authors: Manjari Narayan, Genevera I. Allen, Steffie Tomson.

Markov Network Toolbox for Functional Connectivity.



  • XMRF: An R package to fit Markov Networks to High-Throughput Genetics Data

    • Software to fit Markov Networks to different types of data, encoding the methods for Markov Networks specified via node-conditional univariate exponential family distributions. XMRF supports Gaussian graphical models, Ising models, and four variants of Poisson-family graphical models.

    • Online manual.

    • Authors: Ying-Wooi Wan, Genevera I. Allen, Yulia Baker, Eunho Yang, Pradeep Ravikumar, Zhandong Liu.

    • Citation: Y.W. Wan, G. I. Allen, Y. Baker, E. Yang, P. Ravikumar, and Z. Liu, "XMRF: An R package to Fit Markov Networks to High-Throughput Genetics Data", In ICIBM, 2015.


XMRF: Lung Cancer Gene Expression Network.


  • cvxbiclustr: Convex Biclustering Algorithm.

    • R package.

    • Authors: Eric Chi, Genevera Allen, Rich Baraniuk.


Other Software: