scBatchQC
This is the development version of scBatchQC; to use it, please install the devel version of Bioconductor.
Batch-Aware Cell Quality Control for Single-Cell RNA-seq
Bioconductor version: Development (3.24)
scBatchQC provides a hierarchical empirical Bayes framework for quality control in multi-sample, multi-batch single-cell RNA-seq experiments. Unlike per-sample QC tools, scBatchQC jointly models QC metric distributions (library size, gene count, mitochondrial fraction) and doublet rates across batches, enabling calibrated cell-level QC calls that account for batch structure. The package operates natively on SingleCellExperiment objects and returns augmented colData with per-cell QC flags and batch-adjusted doublet scores.
Author: Subhadip Jana [aut, cre]
Maintainer: Subhadip Jana <subhadipjana1409 at gmail.com>
citation("scBatchQC")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("scBatchQC")
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("scBatchQC")| Batch-aware QC for multi-sample scRNA-seq with scBatchQC | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | BatchEffect, CellBasedAssays, GeneExpression, QualityControl, Sequencing, SingleCell, Software, StatisticalMethod, Transcriptomics, WorkflowStep |
| Version | 0.99.3 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.6.0) |
| Imports | SingleCellExperiment, SummarizedExperiment, BiocParallel, scrapper, methods, stats, S4Vectors, ggplot2, rlang |
| System Requirements | |
| URL | https://github.com/SubhadipJana1409/scBatchQC |
| Bug Reports | https://github.com/SubhadipJana1409/scBatchQC/issues |
See More
| Suggests | scDblFinder, BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0), TENxPBMCData, withr |
| 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 | scBatchQC_0.99.3.tar.gz |
| Windows Binary (x86_64) | scBatchQC_0.99.3.zip |
| macOS Binary (big-sur-x86_64) | scBatchQC_0.99.3.tgz |
| macOS Binary (sonoma-arm64) | scBatchQC_0.99.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scBatchQC |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scBatchQC |
| Bioc Package Browser | https://code.bioconductor.org/browse/scBatchQC/ |
| Package Short Url | https://bioconductor.org/packages/scBatchQC/ |
| Package Downloads Report | Download Stats |