NEWS.md

In whtns/numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

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

whtns/numbat documentation built on Nov. 8, 2022, 10:48 a.m.