Changelog

Source: NEWS.md

cevomod 2.4.0

• code clean-up, unnecessary dependencies removed

cevomod 2.3.0

• subclones can be fitted using CliP (Jiang et al., 2021) (fit_subclones(method = "CliP")). This option requires that the Apptainer is installed. CliP container image can be build with build_clip_container()

cevomod 2.2.0

• fit_powerlaw_tail_fixed() has a bootstrap option

cevomod 2.1.0

• cevomod is integrated with a helper readthis package, designed for bulk reading of variant files from algorithms such as Mutect2, Strelka, ASCAT, or FACETS, in the cevomod-friendly data format. Objects returned by readthis::read_*() functions can be added to the cevodata object using a general add_data() function.

cevomod 2.0.0

• cevomod functions can no utilize VAF or CCF (Cancer Cell Fraction) as a measure of mutation frequency. CCF is calculated using the formula introduced in Dentro et al. Principles of Reconstructing the Subclonal Architecture of Cancers (2015)

cevomod 1.1.0

• cevodata export to CliP implemented

cevomod 1.0.0

• cevodata class implementation
• fitting the power-law tails with exponent equal to 2 using M(f) ∼ 1/f statistic
• fitting the power-law tails with optimized exponent
• fitting subclones using mclust
• fitting subclones using BMix
• calculation of the evolutionary parameters using the Williams et al. (2018) equations and the MOBSTER code (Caravagna et al. (2020))