software

Dendrix: (De novo Driver Exclusivity)

Dendrix is an algorithm for discovery of mutated driver pathways in cancer using only mutation data. It finds sets of genes, domains, or nucleotides whose mutations exhibit both high coverage and high exclusivity in the analyzed samples. This algorithm is described in the paper:

F. Vandin, E. Upfal, B.J. Raphael. (2011) De novo Discovery of Mutated Driver Pathways in Cancer. Genome Research. (In press). Preprint.

[Preliminary version accepted at 15th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2011)]

Download: Dendrix (version 0.1, July 1, 2011)

HotNet: Finding Altered Subnetworks

HotNet is an algorithm for finding significanlty altered subnetworks in a large gene interaction network. This algorithm is described in the paper:

Vandin F, Upfal E, B.J. Raphael . (2011) Algorithms for Detecting Significantly Mutated Pathways in Cancer. Journal of Computational Biology. 18(3):507-22.

[PDF] Publisher Link.

[A preliminary version of the paper appeared at Proceedings of the 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2010). [PDF] ]

Beta versions of HotNet are now available.

  • HotNet (ver0.9.1, June 29, 2011): for finding significantly mutated subnetworks as described in above paper.
  • Generalized HotNet (ver0.9.1, June 29, 2011): a general version of HotNet that allows for arbitrary gene scores.
    • These packages include an early release of a Cytoscape plug-in for visualizing the results. Further updates to this plug-in will be available in Summer 2011.

     

    HotNet and Dendrix Visualization (Cytoscape plug-in)

    A Cytoscape plug-in for viewing HotNet and Dendrix results.

    Download coming soon.

    NBC: Neighborhood Breakpoint Conservation

    This software finds recurrent rearrangement breakpoints in DNA copy number data. The algorithm is described in the paper:

    A. Ritz, P.L. Paris, M.M. Ittmann, C. Collins, and B.J. Raphael. (2011) Detection of Recurrent Rearrangement Breakpoints from Copy Number Data. BMC Bioinformatics. (In Press).

    Geometric Analysis of Structural Variants (GASV)

    Software for analysis of structural variation from paired-end sequencing and/or array-CGH data. This software has been tested used to find structural variation in both normal and cancer genomes using data from a variety of next-generation sequencing platforms. It can be used to predict structural variants directly from aligned reads in SAM/BAM format. The method is described in the following paper:

    S. Sindi, E. Helman, A. Bashir, B.J. Raphael. (2009) A Geometric Approach for
    Classification and Comparison of Structural Variants.Bioinformatics. 25: i222-i230. (Special issue for the Joint 17th Annual International Conference on Intelligent Systems in Molecular Biology and 8th Annual International European Conference on Computational Biology (ISMB/ECCB 09)). Publisher Link

    Old versions. These are for archival purposes. It is recommended to download the latest version from link above.

    • Version 1.4 (3/5/2010) . Download
    • Version 1.3 (1/19/2010) . Download
    • Example BAM file
    • Version 1.2 (11/30/2009) . Download: software
    • New in Version 1.4: Release notes.
    • New in Version 1.3: New output formats, streamlining of BAM file handling, bug fixes.
    • New in Version 1.2 (11/30/2009): Improved handling of SAM/BAM alignment files, speed improvements, maxCliqueSize option.
    • New in Version 1.1: a preprocessor for SAM/BAM files, aCGH comparison, fusion gene detection, and more.
    Motif Description Length (MoDL):

    MoDL finds mutliple motifs in a set of phosphorylated peptides, and is described in the following paper:

    A. Ritz, G. Shakhnarovich, A.R. Salomon, and B. Raphael. Discovery of Phosphorylation Motif Mixtures in Phosphoproteomics Data. (2009) Bioinformatics. 25(1):14-21. Publisher Link

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