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* Added simple examples.
* Added general test statistics, including predefined exclusivity, any co-occurrence, and all co-occurrence test statistics.
* Added optional FDR threshold to `` script to only show significant sets in output.
* Added more accessible random seed to `` script for mutation matrix permutations.
* Updated documentation.

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Weighted Exclusivity Test (WExT)

The Weighted Exclusivity Test (WExT) was developed by the Raphael research group at Brown University.


Latest tested version in parentheses.

  1. Python (2.7.9)

    a. NumPy (1.11.0)

    b. SciPy (0.17.0)

  2. gcc (4.9.2)

We recommend using virtualenv to install the Python requirements. After installing virtualenv, you can install the Python requirements for the weighted exclusivity test as follows:

virtualenv venv
source venv/bin/activate
pip install -r requirements.txt

See the wiki for additional instructions on Setup and installation.


The C and Fortran extensions must be compiled before running the weighted exclusivity test:

cd wext
python build
f2py -c src/fortran/bipartite_edge_swap_module.f95 -m bipartite_edge_swap_module


Data preprocessing

Before computing the weighted test, you need to process the input mutation data and generated permuted matrices.

  1. Process mutation data in MAF format with See Process mutations on the wiki for details on usage and input.
  2. Generate permuted versions of the mutation data -- fixing the number of mutations per gene and per patient/sample -- and compute mutation probabilities with See Compute mutation probabilities on the wiki for details on usage and input.

Searching for exclusive sets

Given the mutation data, we compute the exclusivity of mutations in sets M of genes with Users can choose which test (unweighted, weighted, or permutational) and, for the unweighted and weighted tests, which method (exact or saddlepoint) is used to compute the p-values. See Find exclusive sets on the wiki for details on usage and input.

Searching for exclusive, co-occurring, or other sets

Given the mutation data, we compute the exclusivity, co-occurrence, or other patterns of mutations in sets M of genes with See Find sets on the wiki for details on usage and input.


We provide scripts to run an interactive web application to view the output of, including both the mutations and mutation probabilities for each set. See viz/ and the wiki for additional instructions and details.


See examples for examples, including a simple example that we recommend using for testing.


Please visit the Dendrix Google Group to post questions and view discussions from other users about our methods for identifying mutually exclusive mutations, or contact us through our research group's website.


Mark D.M. Leiserson, Matthew A. Reyna, and Benjamin J. Raphael. (2016) A Weighted Exact Test for Mutually Exclusive Mutations in Cancer. ECCB/Bioinformatics 32(17):i736-745. arXiv preprint

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