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: 2026-03-21 15:45:59 UTC; p032181
Author: Thang Pham [aut, cre, cph, ctb] (ORCID:
    <https://orcid.org/0000-0003-0333-2492>),
  Alex Henneman [ctb] (ORCID: <https://orcid.org/0000-0002-3746-4410>)
Repository: CRAN
Date/Publication: 2026-03-21 16:10:02 UTC
Built: R 4.6.0; x86_64-apple-darwin20; 2026-04-26 20:25:11 UTC; unix
Archs: iq.so.dSYM
