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")):
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("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 |
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) | |
| macOS Binary (big-sur-x86_64) | |
| 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 |