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numbat 1.4.2 - 09/18/2023

• 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

• 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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.