BIOCONDUCTOR . ORG {
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Title:
Bioconductor - limpa
Description:
Quantification and differential analysis of mass-spectrometry proteomics data, with probabilistic recovery of information from missing values. Estimates the detection probability curve (DPC), which relates the probability of successful detection to the underlying expression level of each peptide, and uses it to incorporate peptide missing values into protein quantification and into subsequent differential expression analyses. The package produces objects suitable for downstream analysis in limma. The package accepts peptide-level data with missing values and produces complete protein quantifications without missing values. The uncertainty introduced by missing value imputation is propagated through to the limma analyses using variance modeling and precision weights. The package name
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Keywords {🔍}
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Topics {✒️}
org/packages/limpa source repository joint galaxy/bioconductor conference estimating intensity-dependent probabilities bioconductor release mass-spectrometry proteomics data tgz source repository source packages source package underlying expression level release //code bioconductor support site script reference manual label-free proteomics gz windows binary gordon smyth [cre git clone https tgz macos binary package installed details biocviews statmod system requirements detection probability curve source archive started install proteomics data packages package aut] orcid macos binary software version bioconductor //bioconductor limma analyses smyth gk differential analysis successful detection missing values protein quantification org registration open probabilistic recovery downstream analysis uncertainty introduced variance modeling precision weights linear models cobbold sa quietly = true older versions pdf news
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