scCB2
CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data
Bioconductor version: 3.24 · Package version: 1.23.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
scCB2 is an R package implementing CB2 for distinguishing real cells from empty droplets in droplet-based single cell RNA-seq experiments (especially for 10x Chromium). It is based on clustering similar barcodes and calculating Monte-Carlo p-value for each cluster to test against background distribution. This cluster-level test outperforms single-barcode-level tests in dealing with low count barcodes and homogeneous sequencing library, while keeping FDR well controlled.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scCB2")Details
| Maintainer | Zijian Ni <zni25@wisc.edu> |
| Author | Zijian Ni [aut, cre], Shuyang Chen [ctb], Christina Kendziorski [ctb] |
| License | GPL-3 |
| URL | https://github.com/zijianni/scCB2 |
| Bug Reports | https://github.com/zijianni/scCB2/issues |
| System Requirements | C++11 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, DataImport, GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/scCB2/ |
Citation
From within R, enter citation("scCB2"):
Zijian Ni. scCB2: CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data. doi:10.18129/B9.bioc.scCB2, R package version 1.23.0, https://bioconductor.org/packages/scCB2.
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 | scCB2_1.23.0.tar.gz |
| Windows binary (x86_64) | scCB2_1.23.0.zip |
| macOS binary (arm64) | scCB2_1.23.0.tgz |
| macOS binary (x86_64) | scCB2_1.23.0.tgz |
Dependencies
Depends: R (>= 3.6.0)
Imports: SingleCellExperiment, SummarizedExperiment, Matrix, methods, utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel, iterators, foreach, Seurat
Suggests: testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown