scCB2

DOI: 10.18129/B9.bioc.scCB2    

This is the development version of scCB2; to use it, please install the devel version of Bioconductor.

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

Bioconductor version: Development (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>

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

Installation

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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scCB2")

 

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Details

biocViews Clustering, DataImport, GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 0.99.31
In Bioconductor since BioC 3.12 (R-4.0)
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_0.99.31.tar.gz
Windows Binary scCB2_0.99.31.zip
macOS 10.13 (High Sierra) scCB2_0.99.31.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

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