BUScorrect

DOI: 10.18129/B9.bioc.BUScorrect    

This is the development version of BUScorrect; to use it, please install the devel version of Bioconductor.

Batch Effects Correction with Unknown Subtypes

Bioconductor version: Development (3.8)

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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("BUScorrect", version = "devel")

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 0.99.12
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_0.99.12.tar.gz
Windows Binary BUScorrect_0.99.12.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) BUScorrect_0.99.12.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 http://bioconductor.org/packages/BUScorrect/
Package Downloads Report Download Stats

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