BUSseq

This is the development version of BUSseq; for the stable release version, see BUSseq.

Batch Effect Correction with Unknow Subtypes for scRNA-seq data

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DOI: 10.18129/B9.bioc.BUSseq

Bioconductor version: Development (3.23)

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] ORCID iD ORCID: 0000-0001-6007-3517 , Ga Ming Chan [aut], Yingying Wei [aut] ORCID iD ORCID: 0000-0003-3826-336X

Maintainer: Fangda Song <sfd1994895 at gmail.com>

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

Installation

To install this package, start R (version "4.6") and enter:


if (!require("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.