scCB2

DOI: 10.18129/B9.bioc.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 (3.15)

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 <zni25 at wisc.edu>, Shuyang Chen <zni25 at wisc.edu>, Christina Kendziorski <zni25 at wisc.edu>

Maintainer: Zijian Ni <zni25 at wisc.edu>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("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

PDF   Reference Manual

Details

biocViews Clustering, DataImport, GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.5.0
In Bioconductor since BioC 3.12 (R-4.0) (1 year)
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
Windows Binary
macOS 10.13 (High Sierra)
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/
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