Package: iq 2.1.0

Thang Pham

iq: Protein Quantification in Mass Spectrometry-Based Proteomics

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.

Authors:Thang Pham [aut, cre, cph, ctb], Alex Henneman [ctb]

iq_2.1.0.tar.gz
iq_2.1.0.zip(r-4.7-x86_64)iq_2.1.0.zip(r-4.7-arm64)iq_2.1.0.zip(r-4.6-x86_64)iq_2.1.0.zip(r-4.6-arm64)
iq_2.1.0.tar.gz(r-4.7-arm64)iq_2.1.0.tar.gz(r-4.7-x86_64)iq_2.1.0.tar.gz(r-4.6-arm64)iq_2.1.0.tar.gz(r-4.6-x86_64)
iq_2.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
iq/json (API)

# Install 'iq' in R:
install.packages('iq', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tvpham/iq/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • spikeins - An example dataset of 12 spike-in proteins

On CRAN:

Conda:

cppopenmp

3.72 score 65 scripts 948 downloads 2 mentions 20 exports 2 dependencies

Last updated from:22758813df. Checks:10 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64OK95
linux-devel-x86_64OK104
source / vignettesOK181
linux-release-arm64OK87
linux-release-x86_64OK120
windows-devel-arm64OK201
windows-devel-x86_64OK112
windows-release-arm64OK199
windows-release-x86_64OK98
wasm-releaseOK99

Exports:connected_componentcreate_protein_listcreate_protein_tableextract_annotationfast_MaxLFQfast_preprocessfast_readhuber_weightlong_format_to_iq_formatmaxLFQmeanIntmedian_polishplot_proteinpreprocessprocess_iq_formatprocess_long_formatprocess_matrixprocess_wide_formatrescaletopN

Dependencies:RcppRcppEigen

Fast MaxLFQ
The standard pipeline | A faster MaxLFQ implementation | Benchmarking execution time | An efficient data structure and data loading | References
Rendered fromiq-fast.Rmdusingknitr::rmarkdown

Last update: 2025-10-06
Started: 2020-05-18

Relative protein quantification for DIA-MS-based proteomics
Introduction | Spectronaut output | An example dataset | Protein visualization | Extracting additional protein annotation | OpenSWATH output | Protein quantification | MaxQuant output | Read the protein group data | Building up a protein list from the MaxQuant evidence file | Other quantitation methods: topN, MeanInt, and median polish | References
Rendered fromiq.Rmdusingknitr::rmarkdown

Last update: 2025-10-06
Started: 2019-11-15