Package: numbat 1.4.1

Teng Gao

numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.

Authors:Teng Gao [cre, aut], Ruslan Soldatov [aut], Hirak Sarkar [aut], Evan Biederstedt [aut], Peter Kharchenko [aut]

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NEWS

# Install 'numbat' in R:

install.packages('numbat', repos = c('https://kharchenkolab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kharchenkolab/numbat/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

acen_hg19 - Centromere regions
acen_hg38 - Centromere regions
annot_ref - Example reference cell annotation
bulk_example - Example pseudobulk dataframe
chrom_sizes_hg19 - Chromosome sizes
chrom_sizes_hg38 - Chromosome sizes
count_mat_example - Example gene expression count matrix
count_mat_ref - Example reference count matrix
df_allele_example - Example allele count dataframe
gaps_hg19 - Genome gap regions
gaps_hg38 - Genome gap regions
gexp_roll_example - Example smoothed gene expression dataframe
gtf_hg19 - Gene model
gtf_hg38 - Gene model
gtf_mm10 - Gene model
hc_example - Example hclust tree
joint_post_example - Example joint single-cell cnv posterior dataframe
mut_graph_example - Example mutation graph
phylogeny_example - Example single-cell phylogeny
pre_likelihood_hmm - HMM object for unit tests
ref_hca - Reference expression magnitudes from HCA
ref_hca_counts - Reference expression counts from HCA
segs_example - Example CNV segments dataframe
vcf_meta - Example VCF header

On CRAN:

cancer-genomics cnv-detection lineage-tracing phylogeny single-cell single-cell-analysis single-cell-rna-seq spatial-transcriptomics

16 exports 162 stars 5.05 score 115 dependencies 92 scripts 1.1k downloads

Last updated 4 months agofrom:d21a5b1f47. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 02 2024
R-4.5-win-x86_64	NOTE	Sep 02 2024
R-4.5-linux-x86_64	NOTE	Sep 02 2024
R-4.4-win-x86_64	NOTE	Sep 02 2024
R-4.4-mac-x86_64	NOTE	Sep 02 2024
R-4.4-mac-aarch64	NOTE	Sep 02 2024
R-4.3-win-x86_64	NOTE	Sep 02 2024
R-4.3-mac-x86_64	NOTE	Sep 02 2024
R-4.3-mac-aarch64	NOTE	Sep 02 2024

Exports:aggregate_counts analyze_bulk annotate_genes cnv_heatmap detect_clonal_loh get_bulk get_gtree Numbat plot_bulks plot_consensus plot_exp_roll plot_mut_history plot_phylo_heatmap plot_psbulk plot_sc_tree run_numbat

Dependencies:ape aplot askpass BiocGenerics bitops cachem caTools cli cluster codetools colorspace cpp11 crayon curl data.table dendextend digest dplyr fansi farver fastmap fastmatch fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges getopt ggforce ggfun ggplot2 ggplotify ggraph ggrepel ggtree glue graphlayouts gridExtra gridGraphics gtable hahmmr httr igraph IRanges isoband jsonlite labeling lattice lazyeval lifecycle lobstr logger magrittr MASS Matrix memoise memuse mgcv mime munsell nlme openssl optparse parallelDist patchwork permute phangorn pillar pinfsc50 pkgconfig plyr polyclip prettyunits pryr purrr quadprog R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel reshape2 RhpcBLASctl rlang roptim S4Vectors scales scistreer stringi stringr sys systemfonts tibble tidygraph tidyr tidyselect tidytree treeio tweenr UCSC.utils utf8 vcfR vctrs vegan viridis viridisLite withr XVector yulab.utils zlibbioc zoo

Help page	Topics
centromere regions (hg19)	acen_hg19
centromere regions (hg38)	acen_hg38
Utility function to make reference gene expression profiles	aggregate_counts
Call CNVs in a pseudobulk profile using the Numbat joint HMM	analyze_bulk
example reference cell annotation	annot_ref
Annotate genes on allele dataframe	annotate_genes
example pseudobulk dataframe	bulk_example
chromosome sizes (hg19)	chrom_sizes_hg19
chromosome sizes (hg38)	chrom_sizes_hg38
Plot CNV heatmap	cnv_heatmap
example gene expression count matrix	count_mat_example
example reference count matrix	count_mat_ref
Call clonal LOH using SNP density. Rcommended for cell lines or tumor samples with no normal cells.	detect_clonal_loh
example allele count dataframe	df_allele_example
genome gap regions (hg19)	gaps_hg19
genome gap regions (hg38)	gaps_hg38
Aggregate single-cell data into combined bulk expression and allele profile	get_bulk
Get a tidygraph tree with simplified mutational history.	get_gtree
example smoothed gene expression dataframe	gexp_roll_example
gene model (hg19)	gtf_hg19
gene model (hg38)	gtf_hg38
gene model (mm10)	gtf_mm10
example hclust tree	hc_example
example joint single-cell cnv posterior dataframe	joint_post_example
example mutation graph	mut_graph_example
Numbat R6 class	Numbat
example single-cell phylogeny	phylogeny_example
Plot a group of pseudobulk HMM profiles	plot_bulks
Plot consensus CNVs	plot_consensus
Plot single-cell smoothed expression magnitude heatmap	plot_exp_roll
Plot mutational history	plot_mut_history
Plot single-cell CNV calls along with the clonal phylogeny	plot_phylo_heatmap
Plot a pseudobulk HMM profile	plot_psbulk
Plot single-cell smoothed expression magnitude heatmap	plot_sc_tree
HMM object for unit tests	pre_likelihood_hmm
reference expression magnitudes from HCA	ref_hca
reference expression counts from HCA	ref_hca_counts
Run workflow to decompose tumor subclones	run_numbat
example CNV segments dataframe	segs_example
UPGMA and WPGMA clustering	upgma
example VCF header	vcf_meta

Package: numbat 1.4.1

numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

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