R Observatory: Metrics for parsemsf version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2020-11-17. Its history is shown below.

Reason: check problems were not corrected in time

Details below reflect version 0.1.1, its last release before removal.

parsemsf

0.1.1Package record

Parse ThermoFisher MSF Files and Estimate Protein Abundances

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Benjamin JackCRAN page ↗GitHub ↗

Provides functions for parsing ThermoFisher MSF files produced by Proteome Discoverer 1.4.x (see https://thermofisher.com for more information). This package makes it easy to view individual peptide information, including peak areas, and to map peptides to locations within the parent protein sequence. This package also estimates protein abundances from peak areas and across multiple technical replicates. The author of this package is not affiliated with ThermoFisher Scientific in any way.

Changes in 0.1.1

Added support for dplyr 0.6.0

From NEWS.md in the release

Install

R (source archive)pak (dev)

url <- "https://cran.r-project.org/src/contrib/Archive/parsemsf/parsemsf_0.1.1.tar.gz"
pkgFile <- "parsemsf_0.1.1.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 (0.1.1) 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("benjaminjack/parsemsf")

Development version from benjaminjack/parsemsf. 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 0.1.1

READMEYes · 167 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · mentions 0.1.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 7 (2 internal)includes a package overview page
Examples that run: 83%5 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 83%
Help pages citing references: 0%

How these are measured

Downloads

parsemsf Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on5 autocran

How downloads are counted

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.2.4

Imports (8)

dplyr dbplyr DBI lazyeval RSQLitestatsstringr tidyr

LinkingTo (0)

none

Suggests (4)

testthat knitr rmarkdown ggplot2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Benjamin Jack

Author, Maintainer since 0.1.0 (2017)

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.1.0 released · 2021-05-18
archivedRemoved from CRAN
2020-11-17
check problems were not corrected in time
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
0.1.1
record
2017-12-09 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.1.0
record
2017-01-24
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-01-24
Total releases: 2 / 9 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.2.4

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("parsemsf")

Format

Jack, B. (n.d.). parsemsf: Parse ThermoFisher MSF Files and Estimate Protein Abundances (Version 0.1.1) [Computer software]. Retrieved October 27, 2026, from https://CRAN.R-project.org/package=parsemsf

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 parsemsf version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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