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Please visit https://bitbucket.org/aroth85/pyclone for installation and usage help.

# Versions

## 0.13.1

• Added option to control how clusters are initialized with --init_method flag. Using --init_method connected will 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_clusters flag. For large datasets this should be set to values less than 100 to speed things up.

• Using numba to speed up code.

## 0.13.0

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

• Changed nomenclature.
• 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

## 0.12.9

• Fixed a bug in the calculation of the mpear code.

## 0.12.8

• Fixed a bug causing PyClone BetaBinomial to not support fixed precision parameter.

## 0.12.7

• Fixed bug in multi-sample plotting of allelic prevalences. Note this requires an upgrade to eppl 0.2.3 or greater.

## 0.12.6

• Modified plot_cellular_frequencies to accept the --file_format flag which sets the output format for plot files.

## 0.12.5

• Changed multi sample plot to show error bars

• The build_table no outputs the std error of the cellular prevalence trace for each mutation in each sample

## 0.12.4

• Fixed bug in the multi-sample plotting/table code which caused failures for non PyClone densities.

## 0.12.3

• Added ability to output table used for generating multi-sample plots.

## 0.12.2

• Fixed a bug which would cause build_mutations_file to 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.

## 0.12.1

• 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.

## 0.12.0

• 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_inputs -> build_mutations_file function for building YAML inputs from tsv file.

## 0.11.3

• Fixed overflow in mpear clustering.

## 0.11.1

• Small change to clustering to use mutation_id not mutation in output, to make consistent with simple input.

## 0.11

• Reverted to PyDP for implementing DP methods.

• Removed dependency on numpy in analysis code.

## Older

• Unfortunately I did not keep a complete list of changes as the software evolved.