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", Bioinformatics 32:6, 952-954, 2016. [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.

    • Citation M. Narayan and G. I. Allen, " Mixed Effects Models for Resampled Network Statistics Improves Statistical Power to Find Differences in Multi-Subject Functional Connectivity", Frontiers in Neuroscience, 10:108, 2016. [pdf]

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", BMC Systems Biology, 10(S3):69, 2016. [link]


XMRF: Lung Cancer Gene Expression Network.


  • cvxbiclustr: Convex Biclustering Algorithm.

    • R package.

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

    • Citation: E. C. Chi, G. I. Allen, and R. Baraniuk, "Convex Biclustering", Biometrics, 73:1, 10-19, 2017. [pdf]

  • sCPGA: Sparse Generalized Principal Components Analysis.

    • R package.

    • sGPCA Matlab Toolbox.

    • Authors: Frederick Campbell, Genevera Allen.


    • Citation: G. I. Allen, Logan Grosenick, and Jonathan Taylor, "A Generalized Least Squares Matrix Decomposition", Journal of the American Statistical Association, Theory & Methods, 109:505, 145-159, 2014. [pdf]
  • SpaCCr: Spatial Convex Clustering.

    • R package.

    • Authors: John Nagorski, Genevera Allen.

    • Citation: J. Nagorski and G. I. Allen, ``Genomic Region Detection via Spatial Convex Clustering'', (Submitted), arXiv:1611.04696, 2016. [pdf]

Other Software: