limpa
This is the development version of limpa; to use it, please install the devel version of Bioconductor.
Quantification and Differential Analysis of Proteomics Data
Bioconductor version: Development (3.21)
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 "limpa" is an acronym for "Linear Models for Proteomics Data".
Author: Mengbo Li [aut] (ORCID:
Maintainer: Gordon Smyth <smyth at wehi.edu.au>
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("limpa")For older versions of R, please refer to the appropriate Bioconductor release.
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 |
Details
| biocViews | Bayesian, BiologicalQuestion, DataImport, DifferentialExpression, GeneExpression, MassSpectrometry, Preprocessing, Proteomics, Regression, Software |
| Version | 0.99.10 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| License | GPL (>=2) |
| Depends | limma |
| Imports | methods, stats, data.table, statmod |
| System Requirements | |
| URL |
See More
| Suggests | arrow, knitr, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | limpa_0.99.10.tar.gz |
| Windows Binary (x86_64) | limpa_0.99.10.zip (64-bit only) |
| macOS Binary (x86_64) | limpa_0.99.10.tgz |
| macOS Binary (arm64) | limpa_0.99.10.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/limpa |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/limpa |
| Bioc Package Browser | https://code.bioconductor.org/browse/limpa/ |
| Package Short Url | https://bioconductor.org/packages/limpa/ |
| Package Downloads Report | Download Stats |