proBatch
This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see proBatch.
Tools for Diagnostics and Corrections of Batch Effects in Proteomics
Bioconductor version: Release (3.23)
These tools facilitate batch effects analysis and correction in high-throughput experiments. It was developed primarily for mass-spectrometry proteomics (DIA/SWATH), but could also be applicable to most omic data with minor adaptations. The package contains functions for diagnostics (proteome/genome-wide and feature-level), correction (normalization and batch effects correction) and quality control. Non-linear fitting based approaches were also included to deal with complex, mass spectrometry-specific signal drifts.
Author: Jelena Cuklina [aut], Chloe H. Lee [aut], Patrick Pedrioli [aut], Olga Zolotareva [aut], Yuliya Burankova [cre]
Maintainer: Yuliya Burankova <yuliya.burankova at uni-hamburg.de>
citation("proBatch")):
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")
BiocManager::install("proBatch")
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("proBatch")| proBatch package overview | HTML | R Script |
| ProBatchFeatures: QFeatures-based pipelines with operation logging for proBatch | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, Software, Visualization |
| Version | 2.0.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.5.0) |
| Imports | Biobase, QFeatures, SummarizedExperiment, S4Vectors, corrplot, dplyr, data.table, ggfortify, ggplot2, gridExtra, grDevices, lazyeval, lubridate, limma, magrittr, matrixStats, methods, pheatmap, preprocessCore, purrr, pvca, RColorBrewer, reshape2, rlang, scales, stats, sva, tidyr, tibble, tools, utils, viridis, wesanderson, WGCNA |
| System Requirements | |
| URL | https://github.com/Freddsle/proBatch |
| Bug Reports | https://github.com/Freddsle/proBatch/issues |
See More
| Suggests | BiocStyle, cowplot, ggplotify, knitr, rmarkdown, devtools, gtable, roxygen2, testthat (>= 3.0.0), spelling, HDF5Array |
| 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 | proBatch_2.0.0.tar.gz |
| Windows Binary (x86_64) | proBatch_2.0.0.zip |
| macOS Binary (big-sur-x86_64) | proBatch_2.0.0.tgz |
| macOS Binary (sonoma-arm64) | proBatch_2.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/proBatch |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/proBatch |
| Bioc Package Browser | https://code.bioconductor.org/browse/proBatch/ |
| Package Short Url | https://bioconductor.org/packages/proBatch/ |
| Package Downloads Report | Download Stats |