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

1.8.0Package record

Identifies Signatures Present in a Tumor Sample

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Rachel RosenthalCRAN 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.

Changes in 1.8.0

Changes:

Include function to allow for a VCF file as input
Add parameter in mut.to.sigs.input to allow for alternative genome versions

From NEWS in the release

Install

R (source archive)pak (dev)

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.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.8.0

READMEYes · 865 wordsVignettesNoNEWSYes · 33% structured · mentions 1.8.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 22 (8 internal)includes a package overview page
Examples that run: 67%4 run in a plain check · 2 never run
Exported functions with examples: 43%
Documented parameters: 91%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on141 r2u1.6K bioconda

How downloads are counted

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Rachel Rosenthal

Contributor

Maintainer since 1.5.0 (2016)

Releases (3)

Pick two releases to compare their code metrics.

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
record
2016-07-29 · diff ↗ ·
removed 1 export
findComp

added 1 export
vcf.to.sigs.input
R
R 3.3.0 released · 2016-05-03
1.6.0
record
2016-01-30 · diff ↗ ·
added 1 export
plotTumor
1.5.0
record
2016-01-15
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-01-15
Total releases: 3 / 10 yrs
License: GPL (>= 2) OSI
Bundled data: 103 KB / 7 files

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 October 26, 2026, from https://CRAN.R-project.org/package=deconstructSigs

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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