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 [aut, cre, cph, ctb], Alex Henneman [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:

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