Changes in version 1.5.2 (2026-02-04)                  

  - Replace pryr dependency with base R solution for memory logging
      - Removes deprecated CRAN dependency
      - Uses base R gc() function for memory reporting
      - Maintains identical functionality and output format
      - No user-facing changes

                 Changes in version 1.5.1 (2025-10-21)                  

  - Allow users to input their own GTF (#174)

  - Allow CNV probabilities in segs_consensus_fix parameter (#207)

  - Add multiome analysis helper functions and vignette

  - Improve input validation and error handling

                 Changes in version 1.4.2 (2024-09-20)                  

  - Fix pseudobulk plotting legend (#182)

  - Requirement for dplyr and tidyr versions (#189, #190)

  - Fix Numbat$plot_exp_roll (#169)

  - Fix CNV states reporting when segs_loh is provided (#183)

  - Fix n_states reporting (#178)

  - Improve error handling in pileup_and_phase (#179)

                 Changes in version 1.4.0 (2024-02-23)                  

  - Integration with hahmmr

  - Better input checking for pileup_and_phase

  - Fix compatibility with igraph v2.0+ and tidygraph v1.3+ (#150)

  - Fix multiallelic CNV state probability reporting (#146)

                        Changes in version 1.3.3                        

  - Fix plotting issue #135

  - Fix CRAN check compilation issues

                 Changes in version 1.3.2 (2023-06-06)                  

  - Adding better checks for input files

  - Improve error handling (#122, #127)

                        Changes in version 1.3.1                        

  - Fixing bug #68 - this may cause slight changes in the results for
    runs with segs_loh/call_segs_loh enabled.

                 Changes in version 1.3.0 (2023-04-02)                  

  - Allows users to supply existing CNV profiles (e.g. from bulk WGS/WES
    analysis) via segs_consensus_fix parameter

  - Adding call_clonal_loh option to call clonal LOH events within
    run_numbat

  - Fixing bug #81

  - Fixing oversegmentation issue in find_common_diploid caused by
    annot_segs

                 Changes in version 1.2.2 (2023-02-14)                  

  - Introduce n_cut parameter to specify the number of clones to define
    from the phylogeny

  - Allows users to redefine subclones from the phylogeny via nb$cutree

                 Changes in version 1.2.1 (2023-01-10)                  

  - Fixing bugs #30, #79, #89

                        Changes in version 1.2.0                        

  - Numbat now works for F1 hybrid mice! Check out the new tutorial
    under Articles.

  - Fixing bugs #80, #82

  - Offers stacked clone bars in plot_phylo_heatmap

                 Changes in version 1.1.0 (2022-11-29)                  

  - Externalize phylogeny module as separate package (scistreer)

  - Prepare for new CRAN version

  - Better CNV state legends for plot_bulks

                        Changes in version 1.0.5                        

  - Fixing bugs #65, #66, #67

  - Retire dependency on reshape2

                        Changes in version 1.0.4                        

  - Improving error handling and removing python dependency (argparse)
    in pileup_and_phase.R

  - Allows plotting of mutliple annotations in plot_phylo_heatmap
    (thanks to @whtns)

  - Adding diagnostic messages

                        Changes in version 1.0.3                        

  - Fail gracefully when no CNV remains after retest_bulks

  - Passing gamma parameter to retest_bulks

                 Changes in version 1.0.2 (2022-09-15)                  

  - Conform to CRAN guidelines

  - Removed ATC2 examples from package data - users can download from
    lab server link instead

  - New option to specify genome version (genome = 'hg38' or 'hg19').
    Support plotting of centromeres and gap regions for hg19.

  - Removed genetic maps from package data and they are no longer
    provided as input to run_numbat. Annotation of genetic distance is
    performed in pileup_and_phase.R script instead, using the genetic
    map included in Eagle2.

                        Changes in version 1.0.0                        

  - Archival version for the paper

                        Changes in version 0.1.3                        

  - Speed up of NNI using RcppParallel (#34). 10x faster and much more
    memory efficient (memory requirement is constant with respect to the
    number of threads).

  - Speed up of expression single-cell testing using roptim.
    Approximately 2x speedup.

  - New LLR metric for CNV filtering that is not inflated (default: 5).

  - Only keep heterozygous SNPs in alelle dataframe to reduce memory
    usage