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The single cell genotyper code is provided under the GPLv3 license.
See the attached LICENSE.txt file for more information.
The single cell genotyper is a standard Python package. It can be installed with the following command
python setup.py install
Python >= 2.7.6
panda >= 0.16
numpy >= 1.9.2
scipy >= 0.15
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.
- Added ability to pass initial labels for cells.
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
- Bug fix in position specific doublet model lower bound code
- Minor bug fix in number of events reported to user at the start of run.
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
- Added Dirichlet mixture model
- Fixed doublet implementation to use less memory