limpa
This is the development version of limpa; for the stable release version, see limpa.
All Bioconductor versions of limpa
3.24 (devel), 3.23 (release), 3.22, 3.21
Quantification and Differential Analysis of Proteomics Data
Bioconductor version: 3.24 · Package version: 1.5.2
Quantification and differential analysis of mass-spectrometry proteomics data, with probabilistic recovery of information from missing values. Avoids the need for imputation. Estimates the detection probability curve (DPC), which relates the probability of successful detection to the underlying log-intensity of each precursor ion, and uses it to incorporate missing values into protein quantification and into subsequent differential expression analyses. The package produces objects suitable for downstream analysis in limma. The package accepts precursor (or peptide) intensities including missing values and produces complete protein quantifications without the need for imputation. The uncertainty of the protein quantifications is propagated through to the limma analyses using variance modeling and precision weights, ensuring accurate error rate control. The analysis pipeline can alternatively work with PTM or protein level data. The package name "limpa" is an acronym for "Linear Models for Proteomics Data".
Author: Mengbo Li [aut] 
, Pedro Baldoni [ctb] , Gordon Smyth [cre, aut]
Maintainer: Gordon Smyth <smyth at wehi.edu.au>
Citation
From within R, enter citation("limpa"):
Mengbo Li, Gordon Smyth. limpa: Quantification and Differential Analysis of Proteomics Data. doi:10.18129/B9.bioc.limpa, R package version 1.5.2, https://bioconductor.org/packages/limpa.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("limpa")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.5.2 |
| License | GPL (>=2) |
| URL | https://github.com/SmythLab/limpa |
| Last updated | 2026-09-29 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1 year) |
| Downloads rank | 1902 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bayesian, BiologicalQuestion, DataImport, DifferentialExpression, GeneExpression, MassSpectrometry, Preprocessing, Proteomics, Regression, Software |
| Package Short Url | https://bioconductor.org/packages/limpa/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("limpa")| Analyzing mass spectrometry data with limpa | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | limpa_1.5.2.tar.gz |
| Windows binary (x86_64) | limpa_1.5.2.zip |
| macOS binary (arm64) | limpa_1.5.2.tgz |
| macOS binary (x86_64) | limpa_1.5.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/limpa |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/limpa |
| Package Downloads Report | Download Stats |
Dependencies
Depends: limma
Imports: methods, stats, data.table, statmod
Suggests: knitr, nanoparquet, BiocStyle