Changes in version 0.99.6                        

Bug Fixes

  - Removed incorrect seed parameter from simulateTumor() examples in
    README; use set.seed() before calling the function for
    reproducibility
  - Removed unnecessary library(ggplot2) calls from README, vignette,
    and documentation — ggplot2 is already imported via NAMESPACE and
    loads automatically with the package

                       Changes in version 0.99.0                        

New Features

  - Initial Bioconductor submission
  - Simulate tumor clonal evolution with hierarchical structure
  - Realistic biological noise model using Beta distribution
  - Technical sequencing noise with negative binomial depth variation
  - Binomial sampling for stochastic read counts
  - Sequencing error simulation (Illumina-like)
  - S4 class for simulation results
  - Export to GRanges and VCF formats
  - Comprehensive visualization suite:
      - VAF distribution plots
      - Clonal matrix heatmap
      - Fish plot for temporal evolution
  - Modular, configurable noise parameters
  - Full Roxygen2 documentation
  - Comprehensive vignettes for educational use
  - Unit tests with >80% coverage

Implementation Details

  - Biological heterogeneity modeled with Beta distribution
  - Depth overdispersion with negative binomial distribution
  - Realistic read sampling with binomial distribution
  - Configurable evolutionary hierarchies
  - Support for founder, shared, and private mutations

Future Plans

  - Copy number alteration (CNA) simulation
  - Loss of heterozygosity (LOH) support
  - Subclonal CNA modeling
  - Integration with mutational signature analysis tools