BUSseq

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see BUSseq.

Batch Effect Correction with Unknow Subtypes for scRNA-seq data


Bioconductor version: 3.17

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>

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

Installation

To install this package, start R (version "4.3") 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")
BUScorrect_user_guide PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, Bayesian, Clustering, ExperimentalDesign, FeatureExtraction, GeneExpression, Sequencing, SingleCell, Software, StatisticalMethod
Version 1.6.1
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License Artistic-2.0
Depends R (>= 3.6)
Imports SingleCellExperiment, SummarizedExperiment, S4Vectors, gplots, grDevices, methods, stats, utils
System Requirements
URL https://github.com/songfd2018/BUSseq
Bug Reports https://github.com/songfd2018/BUSseq/issues
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Suggests BiocStyle, knitr, BiocGenerics
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Package Archives

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

Source Package BUSseq_1.6.1.tar.gz
Windows Binary BUSseq_1.6.1.zip (64-bit only)
macOS Binary (x86_64) BUSseq_1.6.1.tgz
macOS Binary (arm64) BUSseq_1.6.1.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 3.17 Source Archive