BUScorrect

DOI: 10.18129/B9.bioc.BUScorrect    

Batch Effects Correction with Unknown Subtypes

Bioconductor version: Release (3.13)

High-throughput experimental data are accumulating exponentially in public databases. However, mining valid scientific discoveries from these abundant resources is hampered by technical artifacts and inherent biological heterogeneity. The former are usually termed "batch effects," and the latter is often modelled by "subtypes." The R package BUScorrect fits a Bayesian hierarchical model, the Batch-effects-correction-with-Unknown-Subtypes model (BUS), to correct batch effects in the presence of unknown subtypes. BUS is capable of (a) correcting batch effects explicitly, (b) grouping samples that share similar characteristics into subtypes, (c) identifying features that distinguish subtypes, and (d) enjoying a linear-order computation complexity.

Author: Xiangyu Luo <xyluo1991 at gmail.com>, Yingying Wei <yweicuhk at gmail.com>

Maintainer: Xiangyu Luo <xyluo1991 at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("BUScorrect")

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("BUScorrect")

 

PDF	R Script	BUScorrect_user_guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, Bayesian, Clustering, FeatureExtraction, GeneExpression, Software, StatisticalMethod
Version	1.10.0
In Bioconductor since	BioC 3.8 (R-3.5) (3 years)
License	GPL (>= 2)
Depends	R (>= 3.5.0)
Imports	gplots, methods, grDevices, stats, SummarizedExperiment
LinkingTo
Suggests	BiocStyle, knitr, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
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	BUScorrect_1.10.0.tar.gz
Windows Binary	BUScorrect_1.10.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	BUScorrect_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BUScorrect
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BUScorrect
Package Short Url	https://bioconductor.org/packages/BUScorrect/
Package Downloads Report	Download Stats