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Changelog

Source: NEWS.md

numbat 1.5.1 - 10/03/2025

CRAN release: 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

numbat 1.4.2 - 09/18/2023

CRAN release: 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)

numbat 1.4.0 - 02/23/2023

CRAN release: 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)

numbat 1.3.3 - 08/15/2023

  • Fix plotting issue #135

  • Fix CRAN check compilation issues

numbat 1.3.2 - 06/05/2023

CRAN release: 2023-06-06

  • Adding better checks for input files

  • Improve error handling (#122, #127)

numbat 1.3.1 - 04/14/2023

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

numbat 1.3.0 - 03/31/2023

CRAN release: 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

numbat 1.2.2 - 02/13/2023

CRAN release: 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

numbat 1.2.1 - 01/11/2023

CRAN release: 2023-01-10

numbat 1.2.0 - 12/26/2022

  • 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

numbat 1.1.0 - 11/28/2022

CRAN release: 2022-11-29

  • Externalize phylogeny module as separate package (scistreer)

  • Prepare for new CRAN version

  • Better CNV state legends for plot_bulks

numbat 1.0.5 - 11/27/2022

  • Fixing bugs #65, #66, #67

  • Retire dependency on reshape2

numbat 1.0.4 - 11/20/2022

  • 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

numbat 1.0.3 - 10/09/2022

  • Fail gracefully when no CNV remains after retest_bulks

  • Passing gamma parameter to retest_bulks

numbat 1.0.2 - 09/07/2022

CRAN release: 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.

numbat 1.0.0 - 08/12/2022

  • Archival version for the paper

numbat 0.1.3 - 07/02/2022

  • 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