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Bioconductor - scCB2 (development version)

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 (3.22)

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 "4.5") 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

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

browseVignettes("scCB2")
CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data HTML R Script Reference Manual PDF NEWS Text Details biocViews Clustering, DataImport, GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics Version 1.19.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 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 See More Package Archives

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

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