The source code for PyClone is now hosted at https://github.com/aroth85/pyclone.
27/09/16 - PyClone 0.13.0 has been released. See the History page for what is new.
14/04/14 - PyClone 0.12.7 has been released. See the History page for what is new.
20/06/13 - PyClone 0.12.3 has been released. See the History page for what is new.
07/06/13 - PyClone 0.12.2 has been released. See the History page for what is new.
06/06/13 - PyClone 0.12.1 has been released. See the History page for what is new.
PyClone is statistical model and software tool designed to infer the prevalence of point mutations in heterogeneous cancer samples. The input data for PyClone consists of a set read counts from a deep sequencing experiment, the copy number of the genomic region containing the mutation and an estimate of tumour content.
Since version 0.12.0 PyClone is able to jointly analyse multiple samples from the same patient.
The current version of PyClone is 0.13.0.
It is strongly suggested you install PyClone using conda with the following command
conda install pyclone -c aroth85. This will install PyClone and the required dependencies.
If you use PyClone please cite
- Roth et al. PyClone: statistical inference of clonal population structure in cancer PMID: 24633410
Look back here soon. The PyClone manuscript has been sent out for review.
History - History of PyClone versions.
Installation 0.13.x - How to install the PyClone 0.13.x software.
Using PyClone 0.13.x - How to use PyClone 0.13.x.
Shah Lab - Homepage for the Shah lab. Check it out for other software developed by our group.
Installation 0.12.x - How to install the PyClone 0.12.x software.
Using PyClone 0.12.x - How to use PyClone 0.12.x.
Tutorial - An example of running a PyClone 0.12.x analysis.
Priors - A brief explanation of how PyClone's 0.12.x
build_mutations_filesets priors for genotypes.
If you need help with PyClone you can post to the user group.
If you find a bug or would like to request a feature please post to the issue tracker on the toolbar above.