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License

The single cell genotyper code is provided under the GPLv3 license. See the attached LICENSE.txt file for more information.

Installation

The single cell genotyper is a standard Python package. It can be installed with the following command

python setup.py install

Dependencies

  • Python >= 2.7.6

  • panda >= 0.16

  • numpy >= 1.9.2

  • scipy >= 0.15

  • PyYaml

For users having difficulty installing Python or the packages required we suggest try the Miniconda (http://conda.pydata.org/miniconda.html) distribution. In addition the pip package for the Python greatly aids in the installation of packages.

Versions

0.3.1

  • Added ability to pass initial labels for cells.

0.3.0

  • Refactored code to be shared between models

  • Added ability to input sample of origin for each cell to obtain sample specific clone proportions

  • Add a work around for numerical issues (or a bug) in the doublet model

0.2.3

  • Minor bug fix.

0.2.2

  • Bug fix in position specific doublet model lower bound code

0.2.1

  • Minor bug fix in number of events reported to user at the start of run.

0.2.0

  • Added position specific version of genotyper models

  • Change CLI so that generating results files is not mandatory

  • Added ability to output a file with just lower bound and convergence of a run

0.1.2

  • Added Dirichlet mixture model

0.1.1

  • Fixed doublet implementation to use less memory

0.1.0

  • Initial release