R Observatory: Metrics for iq version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

iq

2.0.1Package record

Protein Quantification in Mass Spectrometry-Based Proteomics

0packages dependsuggested by 1

9.2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Thang PhamCRAN page ↗GitHub ↗Issues ↗

An implementation of the MaxLFQ algorithm by Cox et al. (2014) doi:10.1074/mcp.M113.031591 in a comprehensive pipeline for processing proteomics data in data-independent acquisition mode (Pham et al. 2020 doi:10.1093/bioinformatics/btz961; Pham et al. 2026 doi:10.1021/acs.jproteome.5c01038). It offers additional options for protein quantification using the N most intense fragment ions, using all fragment ions, the median polish algorithm by Tukey (1977, ISBN:0201076160), and a robust linear model. In general, the tool can be used to integrate multiple proportional observations into a single quantitative value.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("iq", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("tvpham/iq")

Development version from tvpham/iq. Installs pak first if it is not already available.

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-iq

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-iq

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-iq

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.9 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.1

READMENoVignettesYes · 2 · staticNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 20
Examples that run: 50%3 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 26%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 95%

Vignettes (2)

How these are measured

Downloads

9.2K

CRAN downloads in the past year

Rank #3,937 · ~25/day · ~763/mo

Releases R versions

Daily download trend is not available in this view yet.

94730 days

2.3K90 days

9.2K1 year

Compare downloads with other packages →

Also on623 r2u9 autocran565 conda_forge26 c2d4u

How downloads are counted

Repository

tvpham/iq ↗Account: tvpham

34Stars

9Forks

20Open issues

0Open PRs

3Releases

55Commits

4Commit identities

License file reads as BSD-3-Clause · 55 commits · Last activity 2026-03-21 · 0% stars, 30d · Discussions: 2 posts

Responsiveness

How these are sampled

PRs merged (all time): 50%
Median days to close, 50 most recently updated closed issues: 46
Median days to close, 50 most recently updated closed PRs: 4

Stars over time

2025-06-04 · 312026-07-07 · 34

How these are measured

PracticesBeta

Checks run against github.com/tvpham/iq on 2026-10-11.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing iq adds 2 packages (2 with compiled code, 3.5 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppEigen 1.7 MB.

Depends (1)

R >= 2.10

Imports (0)

none

LinkingTo (2)

Rcpp RcppEigen

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

protti

How these are counted

Code & Tests

Datasets

People & History

People (2)

Thang Pham

Alex Henneman

Contributor

Releases (19)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.0.1Latest
record
2026-03-21 · current release · diff ↗
2.0.0
record
2025-10-06 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.10.1
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2024-12-04 · diff ↗
1.10
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2024-12-03 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.9.12
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2023-12-06 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.9.10
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2023-03-29 · diff ↗
1.9.9
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2023-02-27 · diff ↗
1.9.7
record
2023-01-06 · diff ↗
1.9.6
record
2022-04-27 · diff ↗
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2022-04-02
1.9.3
record
2022-04-02 · diff ↗

Show 13 earlier eventsHide 13 earlier events

archivedRemoved from CRAN
2022-02-04
policy violation Misrepresentation of authorship
1.9.1
record
2021-09-15 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.9
record
2020-06-27 · diff ↗
1.8
record
2020-06-14 · diff ↗
1.7
record
2020-05-27 · diff ↗
1.5
record
2020-05-18 · diff ↗
1.4
record
2020-04-27 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.3
record
2020-01-07 · diff ↗
1.1
record
2019-11-16 · diff ↗
1.0
record
2019-11-15
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-11-15
Total releases: 19 / 7 yrs
License: BSD_3_clause + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 137 KB / 1 file
Download size: 450 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("iq")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1021/acs.jproteome.5c01038, 10.1093/bioinformatics/btz961.

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 iq version 2.0.1 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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