numbat
Haplotype-Aware CNV Analysis from scRNA-Seq
Description
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>.
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CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | NOTE |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (8 non-OK)
dependencies in R code
Namespaces in Imports field not imported from: ‘R.utils’ ‘optparse’ ‘vcfR’ All declared Imports should be used.
dependencies in R code
Namespaces in Imports field not imported from: ‘R.utils’ ‘optparse’ ‘vcfR’ All declared Imports should be used.
for GNU extensions in Makefiles
GNU make is a SystemRequirements.
installed package size
installed size is 6.2Mb
sub-directories of 1Mb or more:
data 4.1Mb
for GNU extensions in Makefiles
GNU make is a SystemRequirements.
installed package size
installed size is 6.7Mb
sub-directories of 1Mb or more:
data 4.6Mb
for GNU extensions in Makefiles
GNU make is a SystemRequirements.
installed package size
installed size is 6.3Mb
sub-directories of 1Mb or more:
data 4.1Mb
Check History
NOTE 9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
dependencies in R code
Namespaces in Imports field not imported from: ‘R.utils’ ‘optparse’ ‘vcfR’ All declared Imports should be used.
dependencies in R code
Namespaces in Imports field not imported from: ‘R.utils’ ‘optparse’ ‘vcfR’ All declared Imports should be used.
installed package size
installed size is 6.2Mb
sub-directories of 1Mb or more:
data 4.1Mb
installed package size
installed size is 6.7Mb
sub-directories of 1Mb or more:
data 4.6Mb
installed package size
installed size is 6.3Mb
sub-directories of 1Mb or more:
data 4.1Mb