scCB2

DOI: 10.18129/B9.bioc.scCB2    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see scCB2.

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

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("scCB2")

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("scCB2")

 

HTML	R Script	CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data
PDF		Reference Manual
Text		NEWS

Details

biocViews	Clustering, DataImport, GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.0.0
In Bioconductor since	BioC 3.12 (R-4.0) (0.5 years)
License	GPL-3
Depends	R (>= 3.6.0)
Imports	SingleCellExperiment, SummarizedExperiment, Matrix, methods, utils, stats, edgeR, rhdf5, parallel, DropletUtils, doParallel, iterators, foreach, Seurat
LinkingTo
Suggests	testthat (>= 2.1.0), KernSmooth, beachmat, knitr, BiocStyle, rmarkdown
SystemRequirements	C++11
Enhances
URL	https://github.com/zijianni/scCB2
BugReports	https://github.com/zijianni/scCB2/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	scCB2_1.0.0.tar.gz
Windows Binary	scCB2_1.0.0.zip
macOS 10.13 (High Sierra)	scCB2_1.0.0.tgz
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