R Observatory: Metrics for iq version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

iq

2.0.1

Protein Quantification in Mass Spectrometry-Based Proteomics

1packages depend

10.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Thang PhamFirst published 2019-11-1519 releasesCRAN page ↗GitHub ↗

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.

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).

Health

CRAN checks

13OK

Slowest check: 3.1 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

0

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 50%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 95%

Downloads

10.4K

CRAN downloads in the past year

Rank #4,090 · ~28/day · ~864/mo

Releases R versions

Daily download trend is not available in this view yet.

66330 days

2K90 days

10.4K1 year

Compare downloads with other packages →

Also on626 r2u24 autocran232 conda_forge15 c2d4u

Repository

GitHub ↗ tvpham/iq

34Stars

9Forks

20Open issues

0Open PRs

3Releases

55Commits

4Contributors

License BSD-3-Clause · 55 commits · Last activity 2026-03-21 · 0% stars, 30d

Stars over time

2025-06-04 · 312026-07-07 · 34

Repository practices

Upstream repositoryBeta

Checks run against github.com/tvpham/iq on 2026-08-23.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (0)

none

LinkingTo (2)

Rcpp RcppEigen

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

protti

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Thang Pham

Author, Maintainer, Copyright holder, Contributor

Authors (1)

Thang Pham

Author, Maintainer, Copyright holder, Contributor

Contributors (2)

Thang Pham

Author, Maintainer, Copyright holder, Contributor

Alex Henneman

Contributor

Copyright holders (1)

Thang Pham

Author, Maintainer, Copyright holder, Contributor

Package Timeline

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

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

Show 13 earlier events

archivedRemoved from CRAN
2022-02-04
policy violation Misrepresentation of authorship
1.9.1
2021-09-15 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.9
2020-06-27 · diff ↗
1.8
2020-06-14 · diff ↗
1.7
2020-05-27 · diff ↗
1.5
2020-05-18 · diff ↗
1.4
2020-04-27 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.3
2020-01-07 · diff ↗
1.1
2019-11-16 · diff ↗
1.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("iq")

Format

Pham, T., & Henneman, A. (2026). iq: Protein Quantification in Mass Spectrometry-Based Proteomics (Version 2.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.iq

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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