R Observatory: Metrics for PlasmaMutationDetector version 1.7.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PlasmaMutationDetector

1.7.2Package record

Tumor Mutation Detection in Plasma

0packages depend

2.7Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Yves RozenholcCRAN 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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Yves Rozenholc <yves.rozenholc@parisdescartes.fr>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Yves",
                      family = "Rozenholc",
                      role = c("aut", "cre"),
                      email = "yves.rozenholc@parisdescartes.fr"),
               person(given = "Nicolas",
                      family = "Pécuchet",
                      role = "aut"),
               person(given = "Pierre",
                      family = "Laurent-Puig",
                      role = "aut"))
as necessary.

CRAN check page ↗

Slowest check: 9.5 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-06-27
ERROR10 OK, 2 NOTE, 1 ERROR2026-06-21
NOTE11 OK, 2 NOTE2026-06-11
ERROR11 OK, 1 NOTE, 1 ERROR2026-06-08
NOTE11 OK, 2 NOTE2026-05-10

Show 4 earlier changesHide 4 earlier changes

ERROR10 OK, 2 NOTE, 1 ERROR2026-05-03
NOTE12 OK, 2 NOTE2026-04-16
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-09
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.7.2

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 8
Examples that run: 50%2 run in a plain check · 2 never run
Exported functions with examples: 100%
Documented parameters: 0%
Return-value docs: 100%
Help pages citing references: 100%

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #14,979 · ~7/day · ~226/mo

Releases R versions

Daily download trend is not available in this view yet.

28230 days

80290 days

2.7K1 year

Compare downloads with other packages →

Also on104 r2u

How downloads are counted

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing PlasmaMutationDetector adds 19 packages (8 with compiled code, 16 MB of source tarballs). Heaviest: ggplot2 6.0 MB, robustbase 2.2 MB, isoband 1.5 MB. 6 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (from the free-text Author field) (3)

Yves Rozenholc

Nicolas Pécuchet

Pierre Laurent-Puig

Maintainer since 1.5.2 (2016)

Releases (6)

Pick two releases to compare their code metrics.

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
record
2018-06-11 · current release · diff ↗
1.7.1
record
2018-05-16 · diff ↗
1.7.0
record
2018-04-27 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.6.10
record
2018-01-26 · diff ↗
1.6.2
record
2017-11-15 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.5.2
record
2016-09-09

Show 1 earlier eventHide 1 earlier event

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

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 v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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