proDA
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see proDA.
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
Bioconductor version: 3.13
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>
citation("proDA")
):
Installation
To install this package, start R (version "4.1") 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")
Data Import | HTML | R Script |
Introduction | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | Bayesian, DifferentialExpression, MassSpectrometry, Normalization, Proteomics, QualityControl, Regression, Software |
Version | 1.6.0 |
In Bioconductor since | BioC 3.10 (R-3.6) (4.5 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 |
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.
Source Package | proDA_1.6.0.tar.gz |
Windows Binary | proDA_1.6.0.zip |
macOS 10.13 (High Sierra) | proDA_1.6.0.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 |
Old Source Packages for BioC 3.13 | Source Archive |