1. Andrew Roth
  2. pyclone

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PyClone

News

  • 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.

About

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.

Availability

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.

Citing

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.

Old versions

  • 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_file sets priors for genotypes.

Getting Help

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.

Updated