proBatch
This is the released version of proBatch; for the devel 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")):Jelena Cuklina, Chloe H. Lee, Patrick Pedrioli, Olga Zolotareva. proBatch: Tools for Diagnostics and Corrections of Batch Effects in Proteomics. doi:10.18129/B9.bioc.proBatch, R package version 2.0.0, https://bioconductor.org/packages/proBatch.
Generated from the package metadata; it may differ from the package's own citation.
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 | HTML | R Script |
| ProBatchFeatures | 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, r-universe |
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 |
| Package Short Url | https://bioconductor.org/packages/proBatch/ |
| Package Downloads Report | Download Stats |