Externalize phylogeny module as separate package (
Prepare for new CRAN version
Better CNV state legends for
Improving error handling and removing python dependency (
Allow plotting of mutliple annotations in
plot_phylo_heatmap(thanks to @whtns)
Adding diagnostic messages
Fail gracefully when no CNV remains after
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.Rscript instead, using the genetic map included in Eagle2.
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