BUScorrect
Batch Effects Correction with Unknown Subtypes
Bioconductor version: Release (3.17)
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("BUScorrect")):
Installation
To install this package, start R (version "4.3") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, Bayesian, Clustering, FeatureExtraction, GeneExpression, Software, StatisticalMethod |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.5.0) |
| Imports | gplots, methods, grDevices, stats, SummarizedExperiment |
| Linking To | |
| Suggests | BiocStyle, knitr, RUnit, BiocGenerics |
| System Requirements | |
| Enhances | |
| URL |
See More
| 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_1.18.0.tar.gz |
| Windows Binary | BUScorrect_1.18.0.zip (64-bit only) |
| macOS Binary (x86_64) | BUScorrect_1.18.0.tgz |
| macOS Binary (arm64) | BUScorrect_1.18.0.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 |