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
Bioconductor version: Development (3.21)
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:
Maintainer: Fangda Song <sfd1994895 at gmail.com>
citation("BUSseq")):
Installation
To install this package, start R (version "4.5") 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.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BUSseq")| BUScorrect_user_guide | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, Bayesian, Clustering, ExperimentalDesign, FeatureExtraction, GeneExpression, Sequencing, SingleCell, Software, StatisticalMethod |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 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 |
See More
| Suggests | BiocStyle, knitr, BiocGenerics |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BUSseq_1.13.0.tar.gz |
| Windows Binary (x86_64) | BUSseq_1.13.0.zip (64-bit only) |
| macOS Binary (x86_64) | BUSseq_1.13.0.tgz |
| macOS Binary (arm64) | BUSseq_1.13.0.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 |