proBatch

DOI: 10.18129/B9.bioc.proBatch    

This is the development version of proBatch; for the stable release version, see proBatch.

Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Bioconductor version: Development (3.11)

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: Jelena Cuklina <chuklina.jelena at gmail.com>

Citation (from within R, enter citation("proBatch")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.3.0
In Bioconductor since BioC 3.9 (R-3.6) (0.5 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_1.3.0.tar.gz
Windows Binary proBatch_1.3.0.zip
Mac OS X 10.11 (El Capitan) proBatch_1.3.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: