BUSseq

DOI: 10.18129/B9.bioc.BUSseq    

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

Batch Effect Correction with Unknow Subtypes for scRNA-seq data

Bioconductor version: Development (3.14)

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 "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 0.99.18
In Bioconductor since BioC 3.14 (R-4.1)
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_0.99.18.tar.gz
Windows Binary BUSseq_0.99.18.zip (32- & 64-bit)
macOS 10.13 (High Sierra) BUSseq_0.99.18.tgz
Source Repository git clone https://git.bioconductor.org/packages/BUSseq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BUSseq
Package Short Url https://bioconductor.org/packages/BUSseq/
Package Downloads Report Download Stats

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