proBatch

DOI: 10.18129/B9.bioc.proBatch  

Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Bioconductor version: Release (3.16)

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 <chuklina.jelena at gmail.com>, Chloe H. Lee <chloe.h.lee94 at gmail.com>, Patrick Pedrioli <pedrioli at gmail.com>

Maintainer: Chloe H. Lee <chloe.h.lee94 at gmail.com>

Installation

To install this package, start R (version "4.2") 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")

 

PDF	R Script	proBatch package overview
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, Software
Version	1.14.0
In Bioconductor since	BioC 3.9 (R-3.6) (4 years)
License	GPL-3
Depends	R (>= 3.6)
Imports	Biobase, corrplot, dplyr, data.table, ggfortify, ggplot2, grDevices, lazyeval, lubridate, magrittr, pheatmap, preprocessCore, purrr, pvca, RColorBrewer, reshape2, rlang, scales, stats, sva, tidyr, tibble, tools, utils, viridis, wesanderson, WGCNA
LinkingTo
Suggests	knitr, rmarkdown, devtools, ggpubr, gtable, gridExtra, roxygen2, testthat (>= 2.1.0), spelling
SystemRequirements
Enhances
URL	https://github.com/symbioticMe/proBatch
BugReports	https://github.com/symbioticMe/proBatch/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	proBatch_1.14.0.tar.gz
Windows Binary	proBatch_1.13.0.zip
macOS Binary (x86_64)	proBatch_1.13.0.tgz
macOS Binary (arm64)	proBatch_1.14.0.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
Old Source Packages for BioC 3.16	Source Archive