proBatch

This package is for version 3.16 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: 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>

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

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")
proBatch package overview PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, Software
Version 1.14.0
In Bioconductor since BioC 3.9 (R-3.6) (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
System Requirements
URL https://github.com/symbioticMe/proBatch
Bug Reports https://github.com/symbioticMe/proBatch/issues
See More
Suggests knitr, rmarkdown, devtools, ggpubr, gtable, gridExtra, roxygen2, testthat (>= 2.1.0), spelling
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report 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