wrTopDownFrag

1.0.4

Internal Fragment Identification from Top-Down Mass Spectrometry

0packages depend

2.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Wolfgang RaffelsbergerFirst published 2020-09-082 releasesCRAN 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.

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

Health

CRAN checks

13OK

Slowest check: 2.0 min · r-devel-linux-x86_64-fedora-gcc

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

README

Dependencies · direct

Check history

OK2026-06-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-11
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-10
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Downloads

2.4K

CRAN downloads in the past year

Rank #16,803 · ~6/day · ~197/mo

Releases R versions

Daily download trend is not available in this view yet.

26730 days

68390 days

2.4K1 year

Compare downloads with other packages →

Also on100 r2u

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

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.

Code & Tests

Code Composition

R 3,081 (53%)Rd 2,168 (38%)Vignettes 519 (9%)

Code characteristics

Cyclomatic complexity: 13.0 median / 121 max
Documented parameters: 96%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

40 39 exported

Complexity

20.7 avg / 121 max

Call network

40 nodes / 40 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (1)

Maintainer (1)

Wolfgang Raffelsberger

Author, Maintainer

Authors (1)

Wolfgang Raffelsberger

Author, Maintainer

Release timeline

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

R
R 4.6.0 released · 2026-04-24
1.0.4Latest
2025-04-21 · current release · diff ↗
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
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
Installed size: not tracked yet
With dependencies: not tracked yet