simdms is a script for simulating deep mutational scanning data. These datasets are intended to be analyzed using Enrich2. For more information or to cite simdms, please refer to Enrich2: a statistical framework for analyzing deep mutational scanning data.
simdms runs on Python 2.7 and requires the following packages:
- NumPy version 1.10.4 or higher
- SciPy version 0.16.0 or higher
- pandas version 0.18.0 or higher
- PyTables version 3.2.0 or higher
We recommend using a scientific Python distribution such as Anaconda or Enthought Canopy to install and manage dependencies. PyTables may not be installed when using the default settings for your distribution. If you encounter errors, check that the tables module is present.
To use simdms, git clone or download the repository and run python simdms.py config.json from its root directory. simdms takes a json-formatted configuration file as the command line argument.
Please use the GitHub Issue Tracker to file bug reports or request features.
simdms was written by Alan F Rubin and Hannah Gelman.