R Observatory: Metrics for wrTopDownFrag version 1.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

wrTopDownFrag

1.0.4Package record

Internal Fragment Identification from Top-Down Mass Spectrometry

0packages depend

2.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Wolfgang RaffelsbergerCRAN page ↗

Top-Down mass spectrometry aims to identify entire proteins as well as their (post-translational) modifications or ions bound (eg Chen et al (2018) doi:10.1021/acs.analchem.7b04747). The pattern of internal fragments (Haverland et al (2017) doi:10.1007/s13361-017-1635-x) may reveal important information about the original structure of the proteins studied (Skinner et al (2018) doi:10.1038/nchembio.2515 and Li et al (2018) doi:10.1038/nchem.2908). However, the number of possible internal fragments gets huge with longer proteins and subsequent identification of internal fragments remains challenging, in particular since the the accuracy of measurements with current mass spectrometers represents a limiting factor. This package attempts to deal with the complexity of internal fragments and allows identification of terminal and internal fragments from deconvoluted mass-spectrometry data.

Install

R (CRAN)Ubuntu (r2u)

install.packages("wrTopDownFrag", 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-wrtopdownfrag

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

13OK

CRAN check page ↗

Slowest check: 1.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-08
ERROR12 OK, 1 ERROR2026-06-07
OK13 OK2026-05-11

Show 2 earlier changesHide 2 earlier changes

WARNING12 OK, 1 WARNING2026-05-10
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.4

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 40
Examples that run: 100%40 run in a plain check
Exported functions with examples: 100%
Documented parameters: 96%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

wrTopDownFragVignette1

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #20,151 · ~7/day · ~203/mo

Releases R versions

Daily download trend is not available in this view yet.

28530 days

65590 days

2.4K1 year

Compare downloads with other packages →

Also on76 r2u

How downloads are counted

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing wrTopDownFrag adds 7 packages (2 with compiled code, 6.3 MB of source tarballs). Heaviest: wrProteo 4.6 MB, wrMisc 858 KB, knitr 479 KB. 1 more not on CRAN is not measured.

Depends (1)

R >= 3.1.0

Imports (6)

graphicsgrDevicesstatsutilswrMisc wrProteo

LinkingTo (0)

none

Suggests (7)

BiocParallel knitrparallelpreprocessCore RColorBrewer rmarkdown wrGraph

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 (1)

Wolfgang Raffelsberger

Author, Maintainer since 1.0.2 (2020)

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.4Latest
record
2025-04-21 · current release · diff ↗ ·
removed 1 export
.NtermPepCut

added 15 exports
.chColNa, combinatIntTable, corInDelShift, corMutShift, identifVarModif, identifyPepFragments, modifFragmTabOutput, plotFragmLoc, plotMgfLike, plotPrefFragPat, randMassByMut, randMassByStochastic, scoreFragments, scorePrefFrag, scoreProteinFragments
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
1.0.2
record
2020-09-08
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-09-08
Total releases: 2 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1.0
Download size: 154 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("wrTopDownFrag")

Format

Raffelsberger, W. (2025). wrTopDownFrag: Internal Fragment Identification from Top-Down Mass Spectrometry (Version 1.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.wrTopDownFrag

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 wrTopDownFrag version 1.0.4 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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