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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| Data Import | HTML | R Script |
| Introduction | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, DifferentialExpression, MassSpectrometry, Normalization, Proteomics, QualityControl, Regression, Software |
| Version | 1.27.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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, numDeriv, pheatmap, knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | MatrixQCvis, SmartPhos |
| 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_1.27.0.tar.gz |
| Windows Binary (x86_64) | proDA_1.27.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | proDA_1.27.0.tgz |
| macOS Binary (sonoma-arm64) | proDA_1.27.0.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 |