ProteinBatcher
This is the development version of ProteinBatcher; to use it, please install the devel version of Bioconductor.
An end-to-end proteomics workflow with condition-aware imputation, flexible statistical modelling and interactive visualization
Bioconductor version: Development (3.24)
ProteinBatcher provides utilities to read, validate, and harmonize quantitative proteomics result tables generated by DIA-NN from data-independent acquisition mass spectrometry experiments. The package enables batch processing of multiple DIA-NN output files, consistent handling of protein identifiers and associated metadata, and transformation of tabular data into analysis-ready formats. It facilitates downstream differential abundance analysis using linear modeling frameworks based on limma, with explicit support for multivariable experimental designs including batch effects and other confounding covariates, as well as correlation-aware designs via duplicateCorrelation.
Author: Aitor Moruno-Cuenca [aut, cre]
, Dr. Sergi Sayols-Puig [ctb]
, Dr. Bruna Oriol-Tordera [ctb]
, Dr. Hiba Salim [dtc]
, Dr. Francesc Fernández-Albert [ths]
, Prof. Dr. Alexandre Perera-Lluna [ths]
, Dr. Guadalupe Espadas-García [ctb, dtc]
, Dr. Elisa Monzón-Casanova [ctb, fnd]
, Prof. Dr. Eduard Sabidó-Aguade [res, ctb, dtc, fnd]
Maintainer: Aitor Moruno-Cuenca <morunoaitor at gmail.com>
citation("ProteinBatcher")):
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("ProteinBatcher")
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("ProteinBatcher")| ProteinBatcher workflow | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BatchEffect, DataImport, DataRepresentation, MassSpectrometry, Proteomics, Software |
| Version | 0.99.7 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | data.table, ggplot2, ggrepel, grDevices, grid, limma, methods, S4Vectors, stats, SummarizedExperiment, utils |
| System Requirements | |
| URL | https://github.com/DataScienceRD-Almirall/ProteinBatcher |
| Bug Reports | https://github.com/DataScienceRD-Almirall/ProteinBatcher/issues |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ProteinBatcher_0.99.7.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | ProteinBatcher_0.99.7.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/ProteinBatcher |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ProteinBatcher |
| Bioc Package Browser | https://code.bioconductor.org/browse/ProteinBatcher/ |
| Package Short Url | https://bioconductor.org/packages/ProteinBatcher/ |
| Package Downloads Report | Download Stats |