scCB2

This is the development version of scCB2; for the stable release version, see scCB2.

CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

Bioconductor version: Development (3.19)

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.

Author: Zijian Ni [aut, cre], Shuyang Chen [ctb], Christina Kendziorski [ctb]

Maintainer: Zijian Ni <zni25 at wisc.edu>

Citation (from within R, enter citation("scCB2")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("scCB2")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, DataImport, GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.13.0
In Bioconductor since	BioC 3.12 (R-4.0) (3.5 years)
License	GPL-3
Depends	R (>= 3.6.0)
Imports	SingleCellExperiment, SummarizedExperiment, Matrix, methods, utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel, iterators, foreach, Seurat
System Requirements	C++11
URL	https://github.com/zijianni/scCB2
Bug Reports	https://github.com/zijianni/scCB2/issues

Suggests	testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/scCB2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scCB2
Package Short Url	https://bioconductor.org/packages/scCB2/
Package Downloads Report	Download Stats