miQC
Flexible, probabilistic metrics for quality control of scRNA-seq data
Bioconductor version: 3.23 · Package version: 1.20.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Single-cell RNA-sequencing (scRNA-seq) has made it possible to profile gene expression in tissues at high resolution. An important preprocessing step prior to performing downstream analyses is to identify and remove cells with poor or degraded sample quality using quality control (QC) metrics. Two widely used QC metrics to identify a ‘low-quality’ cell are (i) if the cell includes a high proportion of reads that map to mitochondrial DNA encoded genes (mtDNA) and (ii) if a small number of genes are detected. miQC is data-driven QC metric that jointly models both the proportion of reads mapping to mtDNA and the number of detected genes with mixture models in a probabilistic framework to predict the low-quality cells in a given dataset.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("miQC")Details
| Maintainer | Ariel Hippen <ariel.hippen@gmail.com> |
| Author | Ariel Hippen [aut, cre], Stephanie Hicks [aut] |
| License | BSD_3_clause + file LICENSE |
| URL | https://github.com/greenelab/miQC |
| Bug Reports | https://github.com/greenelab/miQC/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, Preprocessing, QualityControl, Sequencing, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/miQC/ |
Citation
From within R, enter citation("miQC"):
Ariel Hippen, Stephanie Hicks. miQC: Flexible, probabilistic metrics for quality control of scRNA-seq data. doi:10.18129/B9.bioc.miQC, R package version 1.20.0, https://bioconductor.org/packages/miQC.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | miQC_1.20.0.tar.gz |
| Windows binary (x86_64) | miQC_1.20.0.zip |
| macOS binary (arm64) | miQC_1.20.0.tgz |
| macOS binary (x86_64) | miQC_1.20.0.tgz |