R Observatory: Metrics for PlasmaMutationDetector version 1.7.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PlasmaMutationDetector

1.7.2

Tumor Mutation Detection in Plasma

0packages depend

2.5Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Yves RozenholcFirst published 2016-09-096 releasesCRAN page ↗

Aims at detecting single nucleotide variation (SNV) and insertion/deletion (INDEL) in circulating tumor DNA (ctDNA), used as a surrogate marker for tumor, at each base position of an Next Generation Sequencing (NGS) analysis. Mutations are assessed by comparing the minor-allele frequency at each position to the measured PER in control samples.

Install

R (CRAN)Ubuntu (r2u)

install.packages("PlasmaMutationDetector", 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-plasmamutationdetector

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

Slowest check: 9.4 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

9

Dependencies · direct

Check history

NOTE2026-06-27
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-06-11
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-05-10
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-05-03
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-16
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 50%
Documented parameters: 0%
Return-value docs: 100%
References docs: 100%

Downloads

2.5K

CRAN downloads in the past year

Rank #15,080 · ~7/day · ~208/mo

Releases R versions

Daily download trend is not available in this view yet.

20030 days

69190 days

2.5K1 year

Compare downloads with other packages →

Also on172 r2u

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (5)

R >= 3.4.0ggplot2gridGenomicRanges VariantAnnotation

Imports (5)

S4Vectors Rsamtools rtracklayer (>= 1.38.0)robustbase SummarizedExperiment (>= 1.8.0)

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (3)

Pierre Laurent-Puig

no longer listed · 1.5.2 to 1.7.2

Nicolas Pécuchet

no longer listed · 1.5.2 to 1.7.2

Yves Rozenholc

no longer listed · 1.5.2 to 1.7.2

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
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
1.7.2Latest
2018-06-11 · current release · diff ↗
1.7.1
2018-05-16 · diff ↗
1.7.0
2018-04-27 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.6.10
2018-01-26 · diff ↗
1.6.2
2017-11-15 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.5.2
2016-09-09

Show 1 earlier events

R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-09-09
Total releases: 6 / 10 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.4.0
Bundled data: 468 KB / 3 files
Download size: 3.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PlasmaMutationDetector")

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 PlasmaMutationDetector version 1.7.2 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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