Package: iq
Type: Package
Title: Protein Quantification in Mass Spectrometry-Based Proteomics
Version: 2.0.1
Authors@R: c(person("Thang", "Pham", email = "t.pham@amsterdamumc.nl",
                    role = c("aut", "cre", "cph", "ctb"),
                    comment = c(ORCID = "0000-0003-0333-2492")),
             person("Alex", "Henneman",
                    role = c("ctb"),
                    comment = c(ORCID = "0000-0002-3746-4410")))
Maintainer: Thang Pham <t.pham@amsterdamumc.nl>
Description: 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.
Depends: R (>= 2.10)
License: BSD_3_clause + file LICENSE
LinkingTo: Rcpp, RcppEigen
Encoding: UTF-8
LazyData: true
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/tvpham/iq
BugReports: https://github.com/tvpham/iq/issues
NeedsCompilation: yes
Packaged: 2026-06-19 07:56:50 UTC; root
Author: Thang Pham [aut, cre, cph, ctb]
        (<https://orcid.org/0000-0003-0333-2492>), Alex Henneman [ctb]
        (<https://orcid.org/0000-0002-3746-4410>)
Repository: https://tvpham.r-universe.dev
Date/Publication: 2026-03-21 16:14:01 UTC
RemoteUrl: https://github.com/tvpham/iq
RemoteRef: HEAD
RemoteSha: 7540aa71ab2fd176d266798cf404d1d161a35ec1