CRAN/E | numbat

numbat

Haplotype-Aware CNV Analysis from scRNA-Seq

Installation

About

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 . For details on the method please see Gao et al. Nature Biotechnology (2022) doi:10.1038/s41587-022-01468-y.

Citation numbat citation info
github.com/kharchenkolab/numbat/
kharchenkolab.github.io/numbat/
System requirements GNU make

Key Metrics

Version 1.4.0
R ≥ 4.1.0
Published 2024-02-23 35 days ago
Needs compilation? yes
License MIT
License File
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Maintainer

Maintainer

Teng Gao

tgaoteng@gmail.com

Authors

Teng Gao

cre / aut

Ruslan Soldatov

aut

Hirak Sarkar

aut

Evan Biederstedt

aut

Peter Kharchenko

aut

Material

README
NEWS
Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

numbat archive

Depends

R ≥ 4.1.0
Matrix

Imports

ape
caTools
data.table
dendextend
dplyr
GenomicRanges
ggplot2
ggraph
ggtree
glue
hahmmr
igraph
IRanges
logger
magrittr
methods
optparse
parallel
parallelDist
patchwork
pryr
purrr
Rcpp
RhpcBLASctl
R.utils
scales
scistreer ≥1.1.0
stats4
stringr
tibble
tidygraph
tidyr
vcfR
zoo

Suggests

ggrastr
ggrepel
knitr
matrixStats
testthat ≥ 3.0.0

LinkingTo

Rcpp
RcppArmadillo
roptim