proDA

DOI: 10.18129/B9.bioc.proDA  

Differential Abundance Analysis of Label-Free Mass Spectrometry Data

Bioconductor version: Release (3.16)

Account for missing values in label-free mass spectrometry data without imputation. The package implements a probabilistic dropout model that ensures that the information from observed and missing values are properly combined. It adds empirical Bayesian priors to increase power to detect differentially abundant proteins.

Author: Constantin Ahlmann-Eltze [aut, cre] , Simon Anders [ths]

Maintainer: Constantin Ahlmann-Eltze <artjom31415 at googlemail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("proDA")

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("proDA")

 

HTML	R Script	Data Import
HTML	R Script	Introduction
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, DifferentialExpression, MassSpectrometry, Normalization, Proteomics, QualityControl, Regression, Software
Version	1.12.0
In Bioconductor since	BioC 3.10 (R-3.6) (3.5 years)
License	GPL-3
Depends
Imports	stats, utils, methods, BiocGenerics, SummarizedExperiment, S4Vectors, extraDistr
LinkingTo
Suggests	testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr, tibble, limma, DEP, numDeriv, pheatmap, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/const-ae/proDA
BugReports	https://github.com/const-ae/proDA/issues
Depends On Me
Imports Me	MatrixQCvis
Suggests Me	protti
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	proDA_1.12.0.tar.gz
Windows Binary	proDA_1.12.0.zip
macOS Binary (x86_64)	proDA_1.12.0.tgz
macOS Binary (arm64)	proDA_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/proDA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/proDA
Bioc Package Browser	https://code.bioconductor.org/browse/proDA/
Package Short Url	https://bioconductor.org/packages/proDA/
Package Downloads Report	Download Stats