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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>; 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.
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Package details |
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| 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>) |
| Maintainer | Thang Pham <t.pham@amsterdamumc.nl> |
| License | BSD_3_clause + file LICENSE |
| Version | 2.0.1 |
| URL | https://github.com/tvpham/iq |
| Package repository | View on CRAN |
| Installation |
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