BUScorrect

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see BUScorrect.

Batch Effects Correction with Unknown Subtypes


Bioconductor version: 3.9

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>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("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")
BUScorrect_user_guide PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, Bayesian, Clustering, FeatureExtraction, GeneExpression, Software, StatisticalMethod
Version 1.2.1
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License GPL (>= 2)
Depends R (>= 3.5.0)
Imports gplots, methods, grDevices, stats, SummarizedExperiment
System Requirements
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Suggests BiocStyle, knitr, RUnit, BiocGenerics
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BUScorrect_1.2.1.tar.gz
Windows Binary BUScorrect_1.2.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) BUScorrect_1.2.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/BUScorrect
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BUScorrect
Bioc Package Browser https://code.bioconductor.org/browse/BUScorrect/
Package Short Url https://bioconductor.org/packages/BUScorrect/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive