BUSseq

DOI: 10.18129/B9.bioc.BUSseq  

Batch Effect Correction with Unknow Subtypes for scRNA-seq data

Bioconductor version: Release (3.16)

BUSseq R package fits an interpretable Bayesian hierarchical model---the Batch Effects Correction with Unknown Subtypes for scRNA seq Data (BUSseq)---to correct batch effects in the presence of unknown cell types. BUSseq is able to simultaneously correct batch effects, clusters cell types, and takes care of the count data nature, the overdispersion, the dropout events, and the cell-specific sequencing depth of scRNA-seq data. After correcting the batch effects with BUSseq, the corrected value can be used for downstream analysis as if all cells were sequenced in a single batch. BUSseq can integrate read count matrices obtained from different scRNA-seq platforms and allow cell types to be measured in some but not all of the batches as long as the experimental design fulfills the conditions listed in our manuscript.

Author: Fangda Song [aut, cre] , Ga Ming Chan [aut], Yingying Wei [aut]

Maintainer: Fangda Song <sfd1994895 at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("BUSseq")

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("BUSseq")

 

PDF	R Script	BUScorrect_user_guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, Bayesian, Clustering, ExperimentalDesign, FeatureExtraction, GeneExpression, Sequencing, SingleCell, Software, StatisticalMethod
Version	1.4.2
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	Artistic-2.0
Depends	R (>= 3.6)
Imports	SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots, grDevices, methods, stats, utils
LinkingTo
Suggests	BiocStyle, knitr, BiocGenerics
SystemRequirements
Enhances
URL	https://github.com/songfd2018/BUSseq
BugReports	https://github.com/songfd2018/BUSseq/issues
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	BUSseq_1.4.2.tar.gz
Windows Binary	BUSseq_1.4.2.zip (64-bit only)
macOS Binary (x86_64)	BUSseq_1.4.2.tgz
macOS Binary (arm64)	BUSseq_1.4.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BUSseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BUSseq
Bioc Package Browser	https://code.bioconductor.org/browse/BUSseq/
Package Short Url	https://bioconductor.org/packages/BUSseq/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive