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aLFQ specifications


Unique identifier OMICS_04053
Name aLFQ
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.3.4
Stability Stable
plyr, testthat, lattice, data.table, reshape2, seqinr, ROCR, R(≥2.15.0), randomforest, caret, protiq, bio3d
Maintained Yes


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  • person_outline George Rosenberger <>

Publication for aLFQ

aLFQ in publications

PMCID: 5663699
PMID: 29089484
DOI: 10.1038/s41467-017-01422-6

[…] k dil is the dilution rate due to the cell doubling and t cc denotes the cell doubling time (which differs between t1ds and t2n)., the practice of alfq was used. in the present study, to derive absolute protein abundance estimates, 34 anchor proteins covering a wide abundance range in human proteome were targeted by manual data extraction using […]

PMCID: 5566333
PMID: 28827567
DOI: 10.1038/s41467-017-00249-5

[…] multiquant analysis (below) of the sis peptides. protein abundances were inferred by summing the top five most intense fragment ion peak areas from the top three most intense peak groups using the alfq software (v1.33). where <3 peak groups were detected, the available peak groups were summed. coefficients of variation (% cv) were computed as 100*standard deviation/mean. hierarchical […]

PMCID: 4390165
PMID: 25730263
DOI: 10.1038/nm.3807

[…] therefore protein isoforms were excluded. the signals for peptides identified in different samples were aligned along the chromatography prior to label-free protein-level quantification using the alfq r-package . at an estimated false discovery rate of 0.1% at precursor (i.e. ionized peptide) level, we quantified 1,632 unique proteins (). the overall sparsity of the quantified matrix across […]

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aLFQ institution(s)
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland

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