proBatch

This package is for version 3.14 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

DOI: 10.18129/B9.bioc.proBatch

Bioconductor version: 3.14

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 "4.1") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BatchEffect, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, Software

Version 1.10.0

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

Suggests knitr, rmarkdown, devtools, ggpubr, gtable, gridExtra, roxygen2, testthat (>= 2.1.0), spelling

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_1.10.0.tar.gz

Windows Binary proBatch_1.10.0.zip

macOS 10.13 (High Sierra) proBatch_1.10.0.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 3.14 Source Archive