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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>). It offers additional options for protein quantification using the N most intense fragment ions, using all fragment ions, and a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160). In general, the tool can be used to integrate multiple proportional observations into a single quantitative value.

Version: 1.9.12
Depends: R (≥ 2.10)
LinkingTo: Rcpp, RcppEigen
Suggests: knitr, rmarkdown
Published: 2023-12-06
DOI: 10.32614/CRAN.package.iq
Author: Thang Pham ORCID iD [aut, cre, cph, ctb], Alex Henneman ORCID iD [ctb]
Maintainer: Thang Pham <t.pham at amsterdamumc.nl>
BugReports: https://github.com/tvpham/iq/issues
License: BSD_3_clause + file LICENSE
URL: https://github.com/tvpham/iq
NeedsCompilation: yes
Citation: iq citation info
In views: Omics
CRAN checks: iq results

Documentation:

Reference manual: iq.pdf
Vignettes: Fast MaxLFQ
iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics

Downloads:

Package source: iq_1.9.12.tar.gz
Windows binaries: r-devel: iq_1.9.12.zip, r-release: iq_1.9.12.zip, r-oldrel: iq_1.9.12.zip
macOS binaries: r-release (arm64): iq_1.9.12.tgz, r-oldrel (arm64): iq_1.9.12.tgz, r-release (x86_64): iq_1.9.12.tgz, r-oldrel (x86_64): iq_1.9.12.tgz
Old sources: iq archive

Reverse dependencies:

Reverse suggests: protti

Linking:

Please use the canonical form https://CRAN.R-project.org/package=iq to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.