Haplotype-aware CNV analysis from single-cell RNA-seq
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)
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 oversegmentation issue in find_common_diploid
caused by annot_segs
Fixing bug #81
n_cut
parameter to specify the number of clones to define from the phylogenynb$cutree
Numbat now works for F1 hybrid mice! Check out the new tutorial under Articles
.
Fix bugs #80, #82
Offer stacked clone bars in plot_phylo_heatmap
Externalize phylogeny module as separate package (scistreer
)
Prepare for new CRAN version
Better CNV state legends for plot_bulks
Fixing bugs #65, #66, #67
Retire dependency on reshape2
Improving error handling and removing python dependency (argparse
) in pileup_and_phase.R
Allow plotting of mutliple annotations in plot_phylo_heatmap
(thanks to @whtns)
Adding diagnostic messages
Fail gracefully when no CNV remains after retest_bulks
Passing gamma
parameter to retest_bulks
First version on CRAN
Paper archive version :rocket: