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: | 1.10.1 |
| Depends: | R (≥ 2.10) |
| LinkingTo: | Rcpp, RcppEigen |
| Suggests: | knitr, rmarkdown |
| Published: | 2024-12-04 |
| 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 (source) iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics (source) |
Downloads:
| Package source: | iq_1.10.1.tar.gz |
| Windows binaries: | r-devel: iq_1.10.1.zip, r-release: iq_1.10.1.zip, r-oldrel: iq_1.10.1.zip |
| macOS binaries: | r-release (arm64): iq_1.10.1.tgz, r-oldrel (arm64): iq_1.10.1.tgz, r-release (x86_64): iq_1.10.1.tgz, r-oldrel (x86_64): iq_1.10.1.tgz |
| Old sources: | iq archive |
Reverse dependencies:
| Reverse suggests: | protti |
Linking:
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