proBatch
This package is for version 3.9 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: 3.9
The proBatch package facilitates batch effects analysis and correction in high-thoughput 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("proBatch")):
Installation
To install this package, start R (version "3.6") 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 package overview | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, GeneExpression, MassSpectrometry, Normalization, Preprocessing, Proteomics, QualityControl, Software |
| Version | 1.0.0 |
| 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, readr, reshape2, rlang, scales, viridis, stats, sva, tidyr, tibble, utils, wesanderson, WGCNA |
| System Requirements | |
| URL | https://github.com/symbioticMe/proBatch |
| Bug Reports | https://github.com/symbioticMe/proBatch/issues |
See More
| Suggests | knitr, rmarkdown, devtools, roxygen2, testthat |
| 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_1.0.0.tar.gz |
| Windows Binary | proBatch_1.0.0.zip |
| Mac OS X 10.11 (El Capitan) | proBatch_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/proBatch |
| Source Repository (Developer Access) | git clone [email protected]: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 3.9 | Source Archive |