numbat

1.5.2

Haplotype-Aware CNV Analysis from scRNA-Seq

0packages depend

5.4Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Teng GaoFirst published 2022-09-1511 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("numbat", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("kharchenkolab/numbat")

Development version from kharchenkolab/numbat. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-numbat

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 6.1 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-05-10
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-03
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-22
9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-18
8 OK · 5 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
9 OK · 5 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 273 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

5.4K

CRAN downloads in the past year

Rank #8,885 · ~15/day · ~451/mo

Releases R versions

Daily download trend is not available in this view yet.

37630 days

1.2K90 days

5.4K1 year

Compare downloads with other packages →

Also on494 r2u1.6K bioconda

Repository

GitHub ↗ kharchenkolab/numbat

223Stars

35Forks

79Open issues

1Open PRs

10Releases

1,014Commits

12Contributors

cancer-genomicscnv-detectionsingle-cellphylogenysingle-cell-analysissingle-cell-rna-seqspatial-transcriptomicslineage-tracing

1,014 commits · Last activity 2026-02-04 · 0% stars, 30d

Stars over time

2025-07-22 · 1852026-07-07 · 223

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/kharchenkolab/numbat on 2026-07-19.

Continuous integration (2)

GitHub ActionsCircleCI

Reproducibility and dev environment (1)

data-raw/

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

38 external dependencies (excludes base and recommended)

Depends (2)

R >= 4.1.0Matrix

Imports (33)

ape caTools data.table dendextend dplyr GenomicRanges ggplot2 ggraph ggtree glue hahmmr igraph IRanges logger magrittrmethodsoptparseparallelparallelDist patchwork purrr Rcpp RhpcBLASctl R.utils scales scistreerstats4stringr tibble tidygraph tidyr vcfR zoo

LinkingTo (3)

Rcpp RcppArmadillo roptim

Suggests (5)

ggrastr ggrepel knitr matrixStats testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 6,952 (68%)Rd 3,250 (32%)C++ 81 (1%)

Code characteristics

Object systems

R61

Cyclomatic complexity: 2.0 median / 33 max
Test cases: 1 / 0.00 per code line
System requirements: 1 external

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

142 15 exported

Complexity

3 avg / 33 max

Call network

142 nodes / 169 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Datasets

Bundled datasets · 7

Name	Class	Rows × Cols	Also ships in
acen_hg19	tbl_df/tbl/data.frame	22 × 3	in 2 packages
acen_hg38	tbl_df/tbl/data.frame	22 × 3	in 2 packages
annot_ref	data.frame	50 × 2	–
bulk_example	tbl_df/tbl/data.frame	3,935 × 83	–
df_allele_example	data.frame	41,167 × 11	–
gexp_roll_example	data.frame	10 × 2,000	–
vcf_meta	vector	–	in 2 packages

People & History

People (5)

Maintainer (1)

Teng Gao

Maintainer, Author

Authors (5)

Maintainer, Author

Author

Author

Author

Author · added in 1.2.2

Package Timeline

11 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.5.2Latest
2026-02-04 · current release · diff ↗
unarchivedReturned to CRAN
2026-02-04
archivedRemoved from CRAN
2026-01-30
requires archived package 'pryr'
1.5.1
2025-10-21 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.4.2
2024-09-20 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.4.0
2024-02-23 · diff ↗
1.3.2-1
2023-06-17 · diff ↗
1.3.2
2023-06-06 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.3.0
2023-04-02 · diff ↗
1.2.2
2023-02-14 · diff ↗
1.2.1
2023-01-11 · diff ↗
1.1.0
2022-11-29 · diff ↗

Show 2 earlier events

1.0.2
2022-09-15
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-09-15
Total releases: 11 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 3.8 MB / 24 files
Download size: 4.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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