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Bioconductor - proDA (development version)

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 (3.22)

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] ORCID: 0000-0002-3762-068X , Simon Anders [ths] ORCID: 0000-0003-4868-1805

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

Citation (from within R, enter citation("proDA")): 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("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")
Details biocViews Bayesian, DifferentialExpression, MassSpectrometry, Normalization, Proteomics, QualityControl, Regression, Software Version 1.23.0 In Bioconductor since BioC 3.10 (R-3.6) (5.5 years) License GPL-3 Depends Imports stats, utils, methods, BiocGenerics, SummarizedExperiment, S4Vectors, extraDistr System Requirements URL https://github.com/const-ae/proDA Bug Reports https://github.com/const-ae/proDA/issues See More Suggests testthat (>= 2.1.0), MSnbase, dplyr, stringr, readr, tidyr, tibble, limma, DEP, numDeriv, pheatmap, knitr, rmarkdown, BiocStyle Linking To Enhances Depends On Me Imports Me MatrixQCvis Suggests Me protti Links To Me Build Report Build Report Package Archives

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

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