Package: iq 2.0.1

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_2.0.1.tar.gz
iq_2.0.1.zip(r-4.7)iq_2.0.1.zip(r-4.6)iq_2.0.1.zip(r-4.5)
iq_2.0.1.tgz(r-4.6-x86_64)iq_2.0.1.tgz(r-4.6-arm64)iq_2.0.1.tgz(r-4.5-x86_64)iq_2.0.1.tgz(r-4.5-arm64)
iq_2.0.1.tar.gz(r-4.7-arm64)iq_2.0.1.tar.gz(r-4.7-x86_64)iq_2.0.1.tar.gz(r-4.6-arm64)iq_2.0.1.tar.gz(r-4.6-x86_64)
iq_2.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
iq/json (API)
NEWS

# Install 'iq' in R:
install.packages('iq', repos = c('https://tvpham.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

7.09 score 33 stars 47 scripts 748 downloads 2 mentions 19 exports 2 dependencies

Last updated from:7540aa71ab. Checks:11 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING121
linux-devel-x86_64WARNING127
source / vignettesOK182
linux-release-arm64WARNING116
linux-release-x86_64WARNING119
macos-release-arm64WARNING136
macos-release-x86_64WARNING314
macos-oldrel-arm64WARNING135
macos-oldrel-x86_64WARNING349
windows-develWARNING95
windows-releaseWARNING121
windows-oldrelWARNING104
wasm-releaseOK108

Exports:connected_componentcreate_protein_listcreate_protein_tableextract_annotationfast_MaxLFQfast_preprocessfast_readlong_format_to_iq_formatmaxLFQmeanIntmedian_polishplot_proteinpreprocessprocess_iq_formatprocess_long_formatprocess_matrixprocess_wide_formatrescaletopN

Dependencies:RcppRcppEigen

Fast MaxLFQ

Thang V Pham

Rendered fromiq-fast.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2024-12-09
Started: 2020-05-18

Relative protein quantification for DIA-MS-based proteomics

Thang V Pham

Rendered fromiq.Rmdusingknitr::rmarkdownon May 20 2026.

Last update: 2024-12-09
Started: 2019-11-15