numbat 1.4.0 - 10/26/2023

• 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

• 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

• 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

• 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

• Fixing bugs #30, #79, #89

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

• 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

• 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