proDA

DOI: 10.18129/B9.bioc.proDA    

This is the development version of proDA; for the stable release version, see proDA.

Differential Abundance Analysis of Label-Free Mass Spectrometry Data

Bioconductor version: Development (3.11)

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 <artjom31415 at googlemail.com>, Simon Anders <s.anders at zmbh.uni-heidelberg.de>

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

Citation (from within R, enter citation("proDA")):

Installation

To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("proDA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual

Details

biocViews Bayesian, DifferentialExpression, MassSpectrometry, Normalization, Proteomics, QualityControl, Regression, Software
Version 1.1.1
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
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
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository git clone https://git.bioconductor.org/packages/proDA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/proDA
Package Short Url https://bioconductor.org/packages/proDA/
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