R Observatory: Metrics for deconstructSigs version 1.8.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2024-05-14. Its history is shown below.

Reason: issues were not corrected despite reminders

Details below reflect version 1.8.0, its last release before removal.

deconstructSigs

1.8.0

Identifies Signatures Present in a Tumor Sample

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Rachel Rosenthal3 releasesCRAN page ↗GitHub ↗

Takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile.

Install

R (source archive)pak (dev)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/deconstructSigs/deconstructSigs_1.8.0.tar.gz"
pkgFile <- "deconstructSigs_1.8.0.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.8.0) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("raerose01/deconstructSigs")

Development version from raerose01/deconstructSigs. 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-deconstructsigs

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

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

7

Dependencies · direct

Documentation

READMEYes · 865 wordsVignettesNopkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 67%
Documented parameters: 91%
Return-value docs: 100%
References docs: 0%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on99 r2u1.2K bioconda

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (7)

reshape2 BSgenome BSgenome.Hsapiens.UCSC.hg19 GenomeInfoDbgrDevicesgraphicsutils

LinkingTo (0)

none

Suggests (1)

VariantAnnotation

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Other (1)

Rachel Rosenthal

Contributor

Package Timeline

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

R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2024-05-14
issues were not corrected despite reminders
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.8.0
2016-07-29 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.6.0
2016-01-30 · diff ↗
1.5.0
2016-01-15
R
R 3.2.0 released · 2015-04-16

Package metadata

Total releases: 3
License: GPL (>= 2) OSI
Bundled data: 103 KB / 7 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("deconstructSigs")

Format

Rosenthal, R. (n.d.). deconstructSigs: Identifies Signatures Present in a Tumor Sample (Version 1.8.0) [Computer software]. Retrieved August 14, 2026, from https://CRAN.R-project.org/package=deconstructSigs

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for deconstructSigs version 1.8.0 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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