CNSigs

0.1.1

Analysis of Copy Number Signatures

0packages depend

3.2Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Shawn StrikerFirst published 2026-01-082 releasesCRAN page ↗

A workflow to generate and analyze signatures based on copy number data using non-negative matrix factorization (NMF) in an approach similar to that used in mutational signatures. It can be used to extract features from Copy number segment data and use that to find a subset of copy number signatures which can be further used to correlate with other relevant data. For more on 'NMF' see Gaujoux (2013) doi:10.1186/1471-2105-11-367.

Install

R (CRAN)Ubuntu (r2u)

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

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

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-cnsigs

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: 4.9 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 83%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.2K

CRAN downloads in the past year

Rank #7,836 · ~9/day · ~264/mo

Releases R versions

Daily download trend is not available in this view yet.

38530 days

1.4K90 days

3.2K1 year

Compare downloads with other packages →

Also on51 r2u

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (2)

R >= 2.10NMF

Imports (14)

methodsdoParallel foreach flexmix lsei ggplot2 snow cowplot pheatmap RColorBrewer viridisLite colorspacestatsutils

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 2,910 (57%)Rd 1,530 (30%)Vignettes 695 (14%)Other 5 (0%)

Code characteristics

Cyclomatic complexity: 5.0 median / 25 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

41 27 exported

Complexity

7.2 avg / 25 max

Call network

41 nodes / 44 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

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

Datasets

Bundled datasets · 3

Name	Class	Rows × Cols	Also ships in
collapsedSigs	data.frame	29 × 13	–
defaultFeats	vector	–	–
sigExposExp	data.frame	5 × 20	–

8 internal objects are bundled for the package's own use and not listed here.

People & History

People (3)

Maintainer (1)

Shawn Striker

Maintainer, Contributor

Authors (1)

David Tallman

Author

Contributors (1)

Shawn Striker

Maintainer, Contributor

Daniel Stover

Package Timeline

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

0.1.1Latest
2026-06-23 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.1.0
2026-03-10
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-01-08
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 165 KB / 11 files
Download size: 878 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →