PyClone is free for academic/non-profit use. For commercial use please contact email@example.com. Consult the LICENSE.txt file for more details.
Please visit https://bitbucket.org/aroth85/pyclone for installation and usage help.
Added option to control how clusters are initialized with
--init_method connectedwill place all data points in the same cluster leading to faster sampling at the risk of getting stuck in local modes.
Added option to control the maximum number of clusters considered during post-processing using
--max_clustersflag. For large datasets this should be set to values less than 100 to speed things up.
Using numba to speed up code.
Most changes in this release are internal refactoring of the code and should be invisble to the user.
Removed IGMM, IBMM, and IBBMM methods
Changed plotting code to use seaborn
- Removed eppl dependency
- Removed brewer2mpl dependency
Changed output of build_table to a tidy data frame
- Old style table available with the --old_style flag
Re-wrote the multi-sample plotting code
- Should fix issues with too many clusters
- Slightly nicer looking plots
Switched to using pandas for data wrangling
- Variant allele frequency (VAF): proportion of reads with variant
- Cellular prevalence: proportion of cancer cells harbouring a mutation
- The name of the trace files have been altered
- The name of some function calls have been altered
- Plot labels have been altered
- Fixed a bug in the calculation of the mpear code.
- Fixed a bug causing PyClone BetaBinomial to not support fixed precision parameter.
- Fixed bug in multi-sample plotting of allelic prevalences. Note this requires an upgrade to eppl 0.2.3 or greater.
- Modified plot_cellular_frequencies to accept the
--file_formatflag which sets the output format for plot files.
Changed multi sample plot to show error bars
build_tableno outputs the std error of the cellular prevalence trace for each mutation in each sample
- Fixed bug in the multi-sample plotting/table code which caused failures for non PyClone densities.
- Added ability to output table used for generating multi-sample plots.
Fixed a bug which would cause
build_mutations_fileto fail if the output was given as a relative path.
Updated the configuration files in the examples/ folder to have saner values.
Changed README to redirect to website.
Fixed typos in some example files.
Added command to plot parallel coordinates for multiple samples.
Updated interface of plotting commands to take configuration files as arguments instead of traced directory.
Changed input files to work from YAML config instead of command line arguments.
Added ability to do multiple sample analysis.
Added robust Beta-Binomial version of PyClone.
Added genotype naive clustering DP methods with Gaussian, Binomial and Beta-Binomial densities.
Updated and renamed the
build_mutations_filefunction for building YAML inputs from tsv file.
- Fixed overflow in mpear clustering.
- Small change to clustering to use mutation_id not mutation in output, to make consistent with simple input.
Reverted to PyDP for implementing DP methods.
Removed dependency on numpy in analysis code.
- Unfortunately I did not keep a complete list of changes as the software evolved.